Star Trek

I think it gets recycled through the replicator system -- "waste extraction" is matter turned to other random atoms, and then the replicator turns it back to structured matter. When people finish dinner they put their empty plates back into the replicator, which disassembles them.

So in other words, they eat their own poop and dirty dishes. 

On Enterprise, a kid ask command Tucker about it and he said it gets recyled and used to create anything such as boots.

@RomulanValdore, in Enterprise yes. They didn't have replicaters yet.
Replicators are able to covert energy into matter and matter into energy.

So they just put their waste and trash into a replicator which turns it into energy.
Watch Star Trek: Deep Space 9, they often put their plates into a replicator (Food Dispenser). 

Yes, much of it all gets recycled.  Hopefully, the sanitizing filters and ultraviolet cleaners will kill all the germs and other gross things.

Plus, you get a chance to replenish your supplies, when you dock at a spaceport or visit a starbase.

It was basically recycled and re-used as whatever you can think of, as previously mentioned, boots, food, anything the replicator can make. I'm assuming they are sanitary and don't smell like poop, lol.

And if you occasionally did have to jettison some crap into deep space, really, who's going to know?

This is actually something I've thought about a little to often to admit...

It seems obvious that food scraps would go back to the replicators, but toliet waste isn't as obvious, nor nice to think of.

I'm fairly certain that the process of decomposing at the molecular level would kill germs, seeing as it tares them apart atom by atom and converts it to pure energy, so if you don't think about it too much.

I hear Worf gets perverse pleasure out of resequencing the waste atoms into photon torpedos.

It wouldn't very bruident to dispense waste into space. Though Fed engineers can make food & clothing out of thin air.

well, if you use the "Crap" literally, at the right moment, you can confuse the enemy.

Eh... replicators don't sound so nice anymore.... Just don't order anything that is chocolate.... Poor Deanna....

i'm not sure 'confuse' is the right word, but you'd certainly do something to them