Hmmm... 'Running', or 'Installed'?

If all you need is running apps, check the rc files and check the crontab(s) (as well as the services and ports as the other poster mentioned). On BSD, there's also a startup directory /usr/local/etc/rc.d where any script that's executable gets fired off.

If you're looking for what's installed, I'd also do a systemwide sweep of everything in /usr except /usr/src, and look at the magic numbers (first 2 bytes) and shebang lines. Once you have that list, you can identify what's code. Come to think of it, I suppose you could do a first pass look at anything that has its x permission set.