Way back in October Nik (who is busily working on his Aperture 2 review) blogged about the problem combo of Aperture and Time Machine. It would seem that using Time Machine and Aperture could lead to some bad things happening to your Aperture database. Apple's suggestion, at the time, was to simply exclude Aperture's database from your Time Machine backups. Sadly, most photographers like to back up their photographs so this wasn't deemed a long term solution.
Enter OS X 10.5.2 and, according to Apple, the problem is solved. Time Machine will now happily back up your Aperture database (both Aperture 1.5 and 2) without a problem. That sound you hear is thousands of Aperture users breathing a sigh of relief.