They definitely have many stores in large urban centers. Click around on the store list, the majority are mall based.

If your city has a freestanding, non-outlet Gap, Pottery Barn, Crate and Barrel or Williams Sonoma, you are probably worthy of a freestanding Apple store. Otherwise, it will be in an upscale mall near those stores.

In my experience, Apple stores are freestanding in dense urban centers, and located in shopping malls in suburban areas. I haven't seen any exceptions to this rule so far.

That's interesting, I've never seen a single freestanding Apple store before.

Yeah, is there one on the west coast? I know Seattle and Portland's Apple Stores are all in malls.

Freestanding stores are in Palo Alto, Los Gatos, and two in San Francisco.

Just the ones I know offhand.

There's also one inside Stonestown Mall: http://www.stonestowngalleria.com/search?search-query=apple

Two in Chicago (Lincoln Park and Mag Mile), but both of those areas are basically outdoor malls in a loose sense.

All of the Manhattan ones are, obviously.