VeloCult is a must-see, IMO. The largest and most interesting collection of vintage bikes I've seen in one place, especially for mountain bikes. Great beer too.

Clever Cycles on SE Hawthorne has cool cargo and utility bikes. Coventry Cycles, also on SE Hawthorne, has recumbents. River City Bikes has some cool vintage bikes mounted on the walls.

If you're here in summer, look up the Pedalpalooza schedule.