[DirectorTsaarx]

I pretty much follow the "bigger is better" philosophy; once I reach baseships, I use fleets made up of baseships and dreadnoughts. Since I usually take Temporal (better shipyards) and bonuses in construction, it doesn't usually take that much longer to build the bigger ships. My only problem is that dreadnoughts have no defensive penalties, but baseships have a 40% defense penalty; that seems like a big jump to me, even if baseships DO get to use massive weapon mounts...

However, for specialty ships I'll usually use the smaller classes:
Plague ship is frigate or destroyer size (enough room for ECM and stealth/scattering armor, basics and a single plague bomb)
Boarding ship is destroyer or light cruiser
Dedicated point-defense ship is light cruiser or battle cruiser, depending on how big the rest of the ships in the fleet are (and how many seekers/fighters I expect in battle)
Space yard ships are cruisers (obviously), and space yard bases are space stations (again, obviously)

I also tend to stick with medium transports for population moving; they're just the right size for skimming population off 2-3 worlds and then dropping off population on the new colonies. Large transports have to visit 5-7 worlds before they're full (if you're micromanaging population loads).