Thanks for the suggestions everyone; I will try to address all the issues.
You know what else'd take up a hell of a lot of space? Water. Even with purifying systems, they'd need at least supplies for a day or two while the rest of the water was being purified. Now how much does a human need to drink per day? Plus washing, cooking, bathing - times 10 000 on a destoryer? That's a lot of water.
Water would indeed be a space-intensive component, but much more so than that would be the deuterium used to power the ship's reactors. In modern-day space shuttles, fuel accounts for over 95% of the total mass. Also, there are probably some sort of water purifying systems for recycling some of the water, and it is likely that water is used much more sparingly onboard one of these ships than it is on a planet.
Eylsium and Argo are way too high.
Posiden is a little high.
Aten I think should be 200 given its size.
Setekh is a little high
Ma'at is a little high
Aeolus, Charybdis and Triton are too high
Everything else seems right to me.
Could we get the Crew\Passenger thing on there too?
"For the transports, be sure to include passenger space as well as crew space. In the list I think we should have something like this:
ex.
Argo: C20 P85
C=Crew total
P=Maxium passenger capascity."
The Elysium and Argo are indeed too high. I put the Elysium's number at 50, since it is more of a commercial civilian transport than a military vessel and thus has much shorter active periods. (reducing the required supply storage) However, if you put an Argo next to an Orion and compare their proportionate average volumes, combined with the fact that most of the free space in the Argo is used for crew compartments and life support, I think 500 or 600 sounds reasonable.
The Aten's number makes sense, so I will change that one. You are right that the Aeolus is slightly smaller than the other two Terran cruisers, so that has been toned down to 200. Also, I noticed the Mentu is significantly larger than the other GTVA cruisers; I will raise that to 300 or so.
The AWACS ships are essentially the eye of the fleet, tracking enemy ship movements down on radar and sending the information to GTVI. This would probably require lots of personnel to monitor all the sectors and everything. Comparing this with the other ship sizes, I think that while the old numbers were a bit on the high side, 120 or so sounds reasonable.
I halved many of the freighter and gas miner numbers as well. (see below)
In relation to the quoted figure of 6,000 for the corvettes, I could see the Deimos having a maximum capacity in that vicinity. When you compare the Deimos to the Orion you'll notice that the Deimos has a blockier overall shape - if you scale up the Deimos 2.8x so the overall length is equal, you might find it would have a substantually greater volume. The Orion also has to accomodate a fighterbay and room for fighters, plus extra equipment that a fleet flagship would be carrying e.g extra communications equpiment, planetary survey stuff etc. When you consider the modern aircraft carrier and how 5000 sardines are packed onto a 330m ship, again it lends credence that it's certianly not out of reach.
I tried putting up the Deimos next to the Orion, and all things considered, it looks like at least five or six Deimos corvettes could fit inside the Orion's hull. Add that to the fact that the Deimos is designed as a front-line warship rather than an all-purpose command vessel (therefore having big weapon reactors taking up lots of space), I think the original 2000 sounds about right. The main thing with sea-based ships is that they do not need to carry thousands of tons of rocket fuel as space vessels do, thereby freeing up lots of space, but it does indeed serve to show how many men can be packed into a given space.

Something else I thought of, concerning cargo vessels. As karajorma mentoined, in sci-fi (and even IRL) crews of these vessels are small. Why is that the case? Because the more people you have, the more living space and more life support equipment you need. This means less space for cargo - maintaining a high ratio of cargo/overall mass would be quite an important consideration. Otherwise you'd need bigger/more ships. Plus it'd be a waste of personel having dozens of people sitting around doing nothing but watching monitors and playing cards all day.
This certainly makes sense, and I have reduced many of the freighters' numbers accordingly. Same goes for the gas miners, since almost all of the space would be used for storing the collected hydrogen. The one exception might be the Satis, which as I said earlier, is often used as a light escort cruiser or a heavy freighter for transporting sensitive materials, so that would have more. (note how it does not have a cargo dock point; the stuff is probably stored inside) Also, while the Triton is by far the largest of the freighters, it is not really intended for battle and is more for moving around very heavy cargo as stated in the tech room.
All these changes have been made to the above list. Regarding the standard/maximum capacity, I have to go at the moment but I will add those in a bit later. If you have any further comments or suggestions, please post them.