Fun things to do if you know you can't get a captured ship back to friendly territory, and can't risk a ship space yard (or get it there in time):
* Launch/jettison the cargo, immediately!
* Minefield detection/clearing.
* Attacking/blockading nearby ships/planets.
Even a Colony Ship can blockade...
* Colonize a planet and emergency build fighters. They can be fast enough that your enemy, unless very numerous or with his own fighters, can't catch 'em in combat -- and I suspect that a single fighter might be able to blockade a planet...
* Give it to a third party who's also very far away. Especially if the ship is out of fuel, or otherwise crippled. Spread the anger. =) I also do this with PPP'd planets that I can't defend, as well.
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-- The thing that goes bump in the night