How do you backup your websites?
The site code is in Subversion, which is in turn backed up nightly. Any development of the code is done on dedicated dev servers. Production is only updated once the new version has been tested.
The content in relational databases is backed up nightly.
Some of our sites have a huge volume of static content (images, pdfs etc.) and those are stored on RAID5 SANs, mirrored to an offsite facility and have tape backups just in case.
We do not backup log files as we do not rely on them much.
Nightly DB Dump to file
Nightly DB permissions dump to file (Maatkit)
Use Tarsnap for offsite backup of DB dumps plus everything in /var/www/