Using AppleJack, you can repair your disk, repair permissions, validate the system's preference files, and get rid of possibly corrupted cache files. In most cases, these operations can help get your machine back on track.
rsync hfsmode is a patch for rsync to enable recognition of Mac OS X HFS resource forks and Finder metadata, and to copy them to a remote filesystem. The destination system can be any OS and filesystem that supports rsync, so you can use rsync to archive Mac OS X files to servers running Linux, Solaris, et cetera.
Amazon's S3 is an online storage solution; you pay for only what you use ($0.15/GB/month, plus some transfer costs). I wrote a simple step-by-step guide to setting you a Mac to sync with Amazon S3; here's the executive summary version: