I usually don't bother with subfleets; the only times I've ever wished I could control fleet components individually was with the carrier cruisers. (And with Entrenchment, the scouts). Since you can ALT-click to select all ships of a given type, there's not as much need to separate out ship types into subfleets.
That being said, I tend to structure my fleets in complementary ways anyway. For instance, here are the hotkeyed fleets on a large, late-game Vasari:
1> The Offense Fleet: three Desolators, one Marauder, a bunch of transporters (20+) loaded entirely with bombers, and LRM frigates if I use them. Also a couple scouts that accompany the capships instead of going off to sweep.
2-5> The four Defense Fleets: one battleship, one carrier (fighters only), one space egg, a good number (10-20) of heavy cruisers, some flak frigates, a handful (5-10) of transporters loaded mostly with fighters, and a few specialty ships (Overseer, Subverter). These spend their time covering all the front-line systems by way of phase stabilizers, and at least two will ALWAYS be sitting in a system containing an active phase stabilizer.
6-7> Minesweeper subfleets: a half-dozen scouts paired with a half-dozen flak frigates. These not only are useful for minesweeping, they also serve well as "backstop" fleets (when you attack an enemy and he slips a few siege frigates past to hit the recently-vacated planet, this sort of subfleet will defend) so that you don't have to wait for the static defenses to complete before advancing.
8-9> Minelayers, kept in a back-line system untill they're needed.
0> "Battle Fleet", see below.
Usually I don't bother hotkeying colony ships, as phase gates allow me to keep them stockpiled in my home system and send out as needed.
When I'm ready to attack someone I'll group my Offense Fleet, #1, with one of the four Defense Fleets (whichever is closest, least damaged, or most in need of XP), and often one of the minesweeper fleets; this group gets put on hotkey 0. So I'm not attacking with just #1, it's 1, 2, and 6 at the same time, each of which can be maneuvered separately; the combined force is 7 capships of all five types with full support, more than enough for most fights. Then, after the battle is over, I might leave #2 to defend the new system until its stabilizer is complete, send #6 back for repairs, and link 1 up with 3 and 7 to be the new Battle Fleet (redefine hotkey 0) for the next attack. If the new enemy doesn't use heavy mines, I won't even bother with 7, and just pair 1 with 3 alone. And for a REALLY heavy bottleneck fight, I might link two Defense Fleets together... it's flexible.
