I'm overhauling our system backups and am wondering: What files are important to always backup in Windows Server 2003/2008 environments?
Answers to this question will most likely boil down to needing to back up:
On some systems, it's likely not even necessary to back up the system state. Like any backup system, what you back up depends highly on:
Short answer: Don't back up Windows on a file-by-file basis. Use the right tools.
Long answer: This is entirely incumbent on what you're running. IIS stores its configuration differently from Remote Desktop Gateway, for example. Some Windows services have internal databases, where copying off the file may be entirely useless.
There is plenty of software that deals with the tricky stuff for you, and allows you to create a Windows Server backup without too much effort. I recommend a tool that gives you the option for a bare-metal restore, ideally hardware-agnostic. At the low end, Acronis's offerings are your best bet. For larger deployments, I'd use Symantec Backup Exec.