In TNG, the Enterprise-D was able to divide into the saucer section and the bridge section. But no one ever wanted to do that.

In Voyager, they showed (for one episode) the Prometheus (not the same as the Prometheus in DS9) which could divide into three sections, all strong fighters. I don't know how this is an advantage over three ships, but I suppose it is.

But it does bring up one question I'm often troubled by: the Enterprise is fighting some bad guys. They're out numbered. Three ships to one. Scary, right?
So why don't they have a few of their spare pilots take the shuttlecraft/runabouts out to join the fray? They're just sitting their unused, right? Okay, so maybe they have weaker weapons and weaker shields. Maybe they'll get blowed up, along with their pilots, but they lose shuttlecraft every other episode, and what's a couple casulties now and then? Just make sure the pilots are red shirts.