1. Ensure you're fit properly. A $50 eye-ball-it fitting at your LBS is not a proper fit, IMO. Ask around to see who's got a reputation for doing the best fittings. I highly recommend the Retul system, as it can see things the eye can't pick up.
2. Get a good bib/saddle combo. Screw the light weight stuff . . . get something with decent padding to help absorb bumps. Get out of the saddle for the hard bumps.
3. Core exercises. Reverse crunches are awesome. Also do back exercises (as simple as laying on your stomach and raising your feet and shoulders off the ground simultaneously). If you've got a local gym that has one of those contraptions that allows you to bend over, and then raise back up, that's great for focusing on your lower back muscles.
4. A lot of people recommend against serious stretching before working out. I stretch just enough to loosen up so that I don't feel tight on the bike (run in place for a minute to warm up prior to any stretching). But for lower back issues, stretching out your lower back prior to getting on the bike is a good idea. Then, of course, stretch well after riding.