I might as well add my two cents about my experiences with SFC3. First of all, if you add the Dom Wars mod, you get all sorts of better customization options and dozens of new ships. And if you're willing to traipse around in the SPEC files you can do all sorts of interesting things, especially for setting up network games on a router with your friends.
Last year we set up four computers with SFC3 Dom Wars and played as a group. I, as the modder, would usually act as the "alien" (something like a dungeon master) and use weird customizations to make interesting scenarios for my pals to play. Example:
BREEN GHOSTS -- I set the "shuttle" for the Cardassian race (which includes Breen ships) to a small, very weak Breen destroyer, and then changed the flyable Breed Destroyer which was modded to be extremely strong and had 99 shuttles. I let my friends have big battle cruisers and didn't tell them what was going to happen -- just that they were supposed to investigate a Breen R&D facility. As they approached, I kept clocking in and out, launching shuttles, which would cloak in and out on their own (and on my command) so that each cruiser was surrounded by dozens of dopey little ships, cloaking in and out, taking potshot at them. Then I'd periodically uncloak and slam one of their shields. ("WTF was that?") Their challenge was to find me and kill me before I killed them, even though I looked almost identical to every other ship in the game.
THE LOVE BOAT -- I gave my pal (who had just gotten married) a giant Cardassian ship, underpowered it, underweaponed it, and filled it full of marines (passengers). His goal was to fly around a planet (and boy was it sluggish) and deposit all the passengers safely. Meanwhile, the rest of us attacked him with Klingon Birds of Prey. The best part was that I changed the music so that it played "The Love Boat" theme.
ALTERNATE UNIVERSE -- This a weird one. You assign a planetary model to one of the race's shuttles, but without any weapons. Then you up the shuttle count for a ship of that race to 99. Give that ship almost no power. It will keep launching shuttles (i.e. planets) which will continue to roll over one another and "collide" (although they don't have any mass so nothing happens.) Then try to have a battle while flying through the surfaces of the planets. It's like being a world full of giant molecules.
I could go on, but you get the idea.
By the way, the best thing about SFC2/OP is that you don't need a CD to play it, which means that you can run your laptop for 5 hours on a cross country plane flight and still have power to spare! Yay!