My favorite LFS
is The Fish Store, just north of 48th and Vine. It's certainly not the biggest shop but they seem to handle their fish well and stock some unusual specimens from time to time.
Someone mentioned Fish World -- is that the one on Cotner and A in the Piedmont shops? I made my first, and last, visit there a couple weeks ago. They do have some unusual specimens too, but the tanks were poorly kept. I saw several tanks of Ich (oh yeah, there was fish in those tanks, too), dead fish, suffering fish, etc. They did have Bleeding Heart Tetras which I haven't seen for awhile.
The south Petco location, 56th and Hwy 2, is kept up nicely. The other location on O Street... not so much.
Petsmart has a decent selection and is kept up well too. I go there mostly for aquatic supplies more than I do fish.
There's a Pet Ark (or something like that) on 27th and Superior. TERRIBLE store. Every animal in there - fish, cats, birds especially - seem sick and don't present well.
I'll have to check out Aqua Pets next time I'm in Omaha.