When starting our search for an apartment in St. Louis last fall, I bounced from site to site, all the while thinking "there has to be a better way". As it turns out, there is, and it's called PadMapper.
At it's heart, PadMapper is just an aggregator. It scans listings from craigslist, apartments.com, and about a half-dozen other sites and puts them all in once place. That alone is worth the price of admission (free), but it's the filters that really make it useful. First set your maximum price, number of bedrooms, or even limit the commute time to your job. Then, you can flip through the locations on a google map, checking out different neighborhoods.
Bottom line (and I'm not being paid to say this), you should definitely check out PadMapper if you're looking for a new place to rent.