I try to keep these things backed up:
*SQL database
*uploads
*uploads/avatars
Am I missing anything?
Custom theme files, maybe?
Maybe. I'm more looking for files that are modified/updated/uploaded by users on a daily basis.
Well, no PHP files are updated on a daily basis. If I'm not wrong.
maybe do an account backup with your host account and get everything? that is the best way to do a backup
for me i backup all my files
and my database just in case
You should backup all the files in your FTP and download a DB backup from your ACP.