The reason you're seeing listings dominated by the complexes is probably the time of year. I imagine it's the same in Chicago— you'd see a lot more options in May than November. Right now, it's mostly big properties still trying to fill space.
Craigslist is your best bet. Most places you'd have found in the City Paper a decade ago will only be found online now. The apartment rental websites and magazines are only going to list the large management company-owned complexes because that's who's paying the advertising bills.
I often receive requests for housing referrals from my college alumni association and my church, so you might try those avenues. Another source is university newspaper classifieds, but of course they're usually renting for next August at this time of year.
If you're willing to share, your options open up considerably. I have a friend sharing a 4-BR, 4˝ BA townhouse, 3 blocks from the Court House Metro (Orange Line) for about $1000 each. Group houses are extremely common for the under-40 set because that population is so large and transient.
All that said, live close to work/school. The Metro is open late on weekends and cabs are easy to find, but There Is No Good Way To Get There From Here during rush hour if going more than a mile. Driving is impossible unless you get to work before 7am or after 10am. Metrorail is overcrowded and costly, the buses unreliable. As a pedestrian, I have been struck three times by bicylists, of which DC has one of the largest and most self-righteous populations I've seen anywhere. And cyclists endure sticky summers, windy winters, and hatred from motorists, train riders, and pedestrians alike.