It really depends on how you intend to scan the magazines. If you aren't ripping out the pages, then a flat bed scanner without an auto-feeder will be best. My only point of caution is that scanning magazine pages one-by-one is going to be chore in the long run.
I personally use the CanoScan LiDE 200 and recommend it for your application. It's cheap, quick, looks nice, and produces great results. I would check it out in person at your local Best Buy, but deals can be found online.