Let's say you are in command of a fleet of 1000 space-faring ships. When facing the enemy's fleet, what do you deem to be "acceptable losses". To some, acceptable losses may be 25% casualties; for some, winning the battle, regardless of losses.

What would you deem to be acceptable losses in warfare and how can it be justified as such?

how can war be justified? How is it acceptable to command men to go and kill people they've never even met?
There is no straight answer to this. Sometimes war is neccessary, when peace cant move us forward, and there will be casualtys, but there is no number of deaths that are fine. 1 is too many.
From a tactical perspective if you lost about 80% and destroyed all the enemys it would be acceptable. Regardles, once the fights done you can do nothing but accept it, the past is done.
If you won, but didnt have enough force to push forward, or 'hold the fort' per say, that would be a phyric victory, you won but its a hollow victory.
The easiest way to determine if the losses were acceptable is look at the outcome.
Vietnam, lost, evidently the usa lost too many troops to reach the finish line.
Ww2. The allies made it to berlin, so the losses were 'acceptable.'
Nowadays, you cant justify the deaths. Seemingly democratic countrys do backroom deals and fight for money.
There was a time, when 3 continents were set ablaze, that we vowed to end war. How fast the lessons are forgotten.
Casualtys are never acceptable in the sense if it being ok.
The greatest casualty is the wasted potential, and its a slow death.

It really would depend on the situation. I mean, if it was just a war of conquest, I'd say it was very low-why sacrifice men just to own a few more dirtball planets?

However, if it was in defense of the Earth, then it would be anything it took to win the war.

So to really answer your question, I guess I'd need more information as to the context.

Oh it depends.If I would have a homefront whining about every casualty and every person who joined the army by their own free will getting killed, I might think twice even starting the war. Or I would just threaten some other alien species with my ships to do actual work for me. It all comes to the fact that even a single loss of my troops is an unaceptable loss but if a single trooper of mine kills a hundered, thats worth a medal.

So acceptale loss is maybe 1-5%. If they are all poor who nobody cares about anyway or minorities. If not,somebody will get offended that there was a war, somebody joined the ranks as a solider and for some reason, got killed.

What's the objective of the fleet and what's the result of various levels of casualties?  If it takes the last ship to suicide attack another enemy vessel to stop the aliens from wiping out the earth, than 100% casualties is fine.  If vessels need to survive to do something else, less is more important.

AquaFortis66 : its all dependent on what's at stake because there are somethings worth losing everything in order to win and some that aren't even worth a nickel