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Need to do a 'remodel' on my tank. Ideally I'd like to take every piece of rock/coral out of my tank, most of the water, scan the bottom for any think that shouldn't be there ("whoops how'd that piece of copper wire get down there" type stuff), rebuild my reef-scape, then put the water back in, all in a 1 day affair.
However I'd like to minimize fish stress, ideas so far are
1. leave them in there, perhaps even put a rock "cave" in the back corner just so they have some place to hide out
2. remove them, when I'm done, put them back.
3. ????? Other potential ideas would be nice.
-Mike 
Careful if you're going to mess around with the sand/substrate - may want to let things settle before putting livestock back in.
How large is the system and what are the fish? (This is something I do more often than I'd like)
180g tank 4' x 3' foot print. No sand.
-Mike
I would take the fish out and put a lid on whatever you put them into (so nothing jumps). Do your maintenance and then put them back in.
I vote take them out, and the lid is a great idea.
I say drain as much water into a tub, net the fish and put them in the tub (maybe with some clean PVC fitting so the fish have some shelter), do your maintenance, fill the tank back up and return your fish.
Leave the fish
It's one less move they have to deal with
remove the fish IMO. IME you don't want fish in the way of moving rocks and such.
Yeah, considering those fish consist of a couple tangs and a foxface, and I don't need reminding how painful the venom is from that foxface!
Luckily I have more than enough tank space to hold them 
-Mike
Mike,
I would take them all out. I think you would stress them even more by leaving them in the tank with all the movement within the tank.