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Mobile Refinery
These are invaluable for being a drop-off location for your resource collectors who are harvesting far out in space. They can help defend the harvesters but you shouldn't expect them to put up much of a fight. They're more useful for being a diversion until you can get, at the very least, some fighters to help secure the area. Pair one of these with about five workers and set it to guard them (or just park it near the resources you're harvesting). Gun platforms should be used to help secure the area against enemy fighters and keep other resourcers from harvesting in the area.
Probe
I much prefer probes to scouts as they don't take up valuable fighter slots, which could be better used by the much more useful bombers. Probes can move once before they remain stationary and actively watch the area for enemy activity. These can be destroyed rather quickly by enemy ships but the warning they provide is invaluable to your cause. Send a few out to different areas of space to scout out the enemy's location. They have a fairly large sensor range so you will see quite a lot with them. Use knowledge of enemy resource positions that are relatively unguarded to deliver a swift economic victory. I generally ignore enemy mobile refineries and take out the resource collectors. The refineries take too long to kill with interceptors and you can run away after the harvesters are dead.
Proximity Sensor Probe
Proximity probes have a reduced sensor range than that of standard probes but have the capability to detect cloaked vessels. You probably won't run into many cloaked ships during the course of your gameplay, but if you do, this is one of the ways to detect them without using a sensors slot on one of your capital ships. It might be wise to have one of these on standby to send if you suspect cloaked enemy ships, but I usually don't even bother doing that.
Resource Collector
Resource collectors are vital to your economic prosperity. You need them to harvest resources for the construction of ships. They should be protected by mobile refineries and possibly some gun turrets. Always have some fighters hotkeyed to help protect them should they come under attack. With the repair upgrade, these can repair your capital ships rather quickly in groups. That being said, you might want to have a couple hotkeyed to repair that battlecruiser or dreadnought before it heads into its next battle!
Sensors Distortion Probe
These are almost useless against other players but do tend to confuse the AI somewhat. They create a dust cloud effect which makes enemy ships have to be pretty darn close to detect your ships. Only the ships within the range of the probe have distorted sensor readings, however. You should experiment with these as I generally don't use them much. One benefit to them is that they have a much larger sensor range than standard probes. This comes at a higher cost in resources and a longer build time.
Scout
As the name implies, the Hiigaran scout is primarily used for scouting out enemy locations. They're cheap and disposable so you won't feel a great loss when a squadron is destroyed. Their speed makes them capable of a quick getaway when necessary. These can be used to have a peek at enemy positions before you send in a strike group. Unfortunately for the scout, their use is limited due to the fact that you could simply send in a probe to complete such a task. Their usefulness in combat is comparable to a probe simply because they are poorly armed and armored. It would take a long time for a squadron of scouts to take out dedicated enemy combat vessels. The scouts do have a couple redeeming qualities that may make them useful to you.
The scout has two abilities. One is to ping the sensors. This ability costs 1000 RU and will reveal the location of all enemy ships. This can be quite useful for just before you launch your attack, to keep an eye on any unwanted suprises. The second skill of the scout is the EMP ability. When utilized, the scout fires off an electromagnetic pulse which disables enemy ships. Be forewarned, however, that it takes many scouts to overwhelm a captial ship. That being said, they don't really hold their own in combat because valuable fighter slots would be taken up to have enough scouts to disable a dreadnought. Bombers would be better suited to the task than scouts, in my opinion, but you may discover that they suit your play style. I almost never use them.
Interceptor
Interceptors are the standard fighter for the Hiigarans. They're quite useful for quickly reinforcing harvesters who come under attack by enemy fighters as well as drawing fire in fleet engagements. Their speed makes them likely to be the first units in an engagement, which can be a drawback if you're not careful. Unfortunately, their weapons are almost useless against anything larger than a corvette. Still, these are great for filling out your fighter slots with what's left over after you've made bombers. They should always be present when your bombers are at work to draw fire and protect them from enemy fighters, which will rip your bombers to shreds.
Bomber
Bombers are an invaluable tool no matter how far up the tech tree you are in Homeworld 2. They're designed to take out enemy frigates and capital ships, plain and simple. Their bombs are useless against fast-moving targets so it's extremely important that you defend them against fighters and corvettes. Several squadrons can take out a frigate in just a few attack runs. They're not so fast at taking out destroyers and battlecruisers but the larger ships will be hard pressed to hit them. With the improved bombs upgrade they can place their bombs with precision, eliminating enemy capital ships' subsystems very quickly. Do not underestimate the ability to eliminate a battlecruiser's engines and missile launchers. Protect your bombers and they will serve you well.
Gunship
Gunships are great at tearing up enemy fighter and bomber formations. They're better armored than interceptors, but are also a lot slower. The speed reduction makes them more vulnerable to enemy weapon fire but their 360-degree turrets make their lack of maneuverability a non-issue in regard to keeping the enemy under fire. They're unfortunately not that powerful in combat, however, and other ship types are better suited to taking out fighters. Still, they're a good way to fill out your corvette slots. You should probably use pulsar gunships primarily as your corvette-class ship due to the fact that there are other ships better able to eliminate fighters.
Pulsar Gunship
Pulsar gunships are suited to eliminate other corvettes. Their description says they're good at taking out frigates, too, but that isn't their best role in combat. Pulsars are your friends because of their swift destruction of corvettes and you should fill out quite a lot of your corvette slots with them if the enemy is using many of that class of vessel. Pulsars can take on frigates when all the corvettes are destroyed, so they are somewhat versatile in combat.
Minelayer Corvette
Minelayers do just what you'd suspect, lay mines. You can select where the mines are to be laid and what size the field will be when complete. When the minelayer is done making a field, it will continually replace the mines in the field. Mines have a timed countdown before they disappear, so the minelayer will replace them one at a time. If you see enemy ships approaching your minelayers, boogie. The minelayers are almost defenseless. You might even lure the enemy through your minefield, destroying them in the process.
Defense Field Frigate
Defense field frigates project a defensive field which reduces damage to all ships within the field. The only drawback is that enemy ships that pass the barrier of the field will do full damage. The primary use then is to help protect ships from long range fire. Focus your ships' weapons on the enemies that pass within the field so that they can be more quickly eliminated. This ship is invaluable for destroyer on destroyer combat as the destroyer behind the field is sure to win if they started at equal health. The field is only active a short time before it must be reactivated. There is a cooldown time where the frigate must recharge the field. You'll have to manually activate the field each time by using the 't' hotkey.
Flak Frigate
These bad boys can take down fighters really swiftly when they're used in groups. Unfortunately, other frigates will make quick work of them. They're very useful for protecting your capital ships from enemy bombers, along with your fighters. You will almost always want a couple of these in your fleet. It's almost sick watching them lay waste to puny little ships. Take note, they're almost completely ineffective against anything bigger than a corvette.
Ion Cannon Frigate
Ion cannon frigates should almost always be present when you intend to fight other frigates or capital ships. They're not very well armored considering the type of ship they're supposed to destroy but they can certainly dish the damage. Groups of six or more are capable of taking out a destroyer with a little help with bombers. Like other frigates, they're painfully slow and you will want to carefully place them in combat so they can avoid having to move a lot to utilize their ion cannons. The ion beams these fire have a very hard time hitting anything smaller than a frigate but other ships can deal with that type of enemy. Take note when using them that you might not want to concentrate all their firepower on a single dreadnought. You should take out frigates because you can more quickly eliminate enemy firepower.
Marine Frigate
Marine frigates are used to capture enemy ships. They can capture anything larger than corvettes (frigates, dreadnoughts, battlecruisers), but the larger the ship, the longer the time it will take to capture it. You can use multiple marine frigates to more quickly capture enemy ships. If you cancel the infiltration operation it will reset the timer, so try to keep them locked on. Also, protect them as they can be destroyed while in the middle of the operation, and it's highly likely. Who wouldn't focus on these when they're trying to capture a battlecruiser?
Torpedo Frigate
This is one type of ship I'm really not that fond of. You can use them to attack corvettes (good) or enemy frigates (not so good). They'll need the improved torpedoes to tackle frigates and larger, and even then they're not that great at the job. With Pulsar gunships around to eliminate corvettes, who needs these? Also, Ion frigates are much better at destroying frigates. I really can't say much for these. At least they are capable of eliminating multiple types of ships, but other ships are just plain better at it.
Gun Platform
In numbers, these can really help to soften up fighters and corvettes attacking your positions. They're good to help mobile refineries defend valuable resource locations. At the least, they can hold off the enemy until your interceptors come to repel the attack. Keep in mind that these can only be moved once before they're deployed and become immobile. Position them carefully.
Ion Cannon Platform
Ion cannon platforms are good at helping to both soak damage and weaken enemy frigates. Generally they have trouble hurting dreadnoughts much before they are destroyed, but they can still take some damage. Don't expect to get by with just one of these. It's much more wise to build them in pairs, at least, and keep them with a gun platform or two to help against fighters. It's useful to have a couple around near your mothership so that they can help defend it should the enemy attack you. Like gun platforms, these can be moved only once before they're 'deployed' and become immobile. Position them carefully. I like to put a couple just ahead of where ever I've parked my mothership.
Battlecruiser
This monster can turn the tide of any battle against anything larger than corvettes. They're almost useless against small ships but eat up large ships. Its big guns will bring down dreadnoughts quite quickly and make short work of enemy frigates. The ship can be outfitted with a fire control module to boost the combat effectiveness of all friendly ships in the area. You could even put a hyperspace module on it to help it jump into combat and chase down that fleeing enemy mothership. These aren't to be taken lightly and losing one is a big deal. They can only be constructed at a shipyard due to their massive size. This is the most powerful ship in the game. If you're going to invest in one of these be sure to upgrade its armor and speed so that it can be much more effective in combat. I really do recommend the hyperspace module and fire control tower combination. If the battlecruiser gets into trouble you can probably have enough time to hyperspace it out at least a short distance to keep it safe from the enemy while your resource collectors repair it. Don't let this thing go into combat alone. Its style of attack makes it highly vulnerable to enemy bombers. It can stand up for a long time before it falls but it will fall.
Carrier
Carriers are your secondary production ships. They can produce everything but other capital ships and can be used in a variety of ways. The most common is to simply keep them near your mothership to boost your production. Another way to use them is to bring them along in an assault, keeping them behind the lines to help reinforce lost ships in a battle. They are capable of hyperspacing so they could be used to jump frigates and destroyers into a battle to help reinforce it from afar. This isn't cheap, however and if you wasted the RUs you might find yourself on the defensive fairly quickly if the battle is lost.
Dreadnought
Dreadnoughts are the battlecruiser's little brother. They crumble frigates like there's no tomorrow and can take up a lot of damage before they're destroyed. The only thing that can take this bad boy out quickly is another destroyer and even then it's going to be a tough fight. It's highly recommended you upgrade the armor on this ship because at such a high starting value it gains a lot from even the level one upgrade. A speed increase is in order as well because they are painfully slow.
Mothership
Your starting ship. If you lose it, you're toast. The mothership can build four production facilities. It has a lot of hit points but is far from invincible. It's extremely slow, as you might expect. It's also not very good at defending itself, so keep it safe. I usually avoid the platform control module so the mothership can pump out mobile ships while carriers handle the platform production. Never leave your mothership completely undefended unless you're feeling cocky.
Shipyard
The shipyard is the only class of ship which is capable of producing Battlecruisers. You can only posess one of these monsters at a time, which is reasonable. This vessel is so large it's warped in, rather than constructed. The shipyard can handle six modules on its massive hull, so you can utilize every one of the Hiigaran upgrades. Still, the shipyard shouldn't be taken into battle. You want to protect it because it's very expensive and very valuable to reinforcing your fleet. With this and the mothership you can produce two dreadnoughts at once. With the improved manufacturing research upgrade on both the mothership and this beast, you'll be pumping out dreadnoughts like crazy. It's just too bad you can only support five at once. When I warp in a shipyard I always start building a capital class facility asap, provided I can afford it.