As previously mentioned, the robots.txt spec is pretty simple. However, one thing that I've done is create a dynamic script (PHP, Python, whatever) that's simply named "robots.txt" and have it smartly generate the expected, simple structure using the more intelligent logic of the script. You can walk subdirectories, use regular expressions, etc.
You might have to tweak your web server a bit so it executes "robots.txt" as a script rather than just serving up the file contents. Alternatively, you can have a script run via a cron job that regenerates your robots.txt once a night (or however often it needs updating)