I'd love a response to this one myself, but I can tell you some of the things that I've learned so far:

-FLAdmin will restart your server automagically if it crashes and let you (sort of) remotely control your server. I personally use Terminal Services though.
-FLPing will tell you remotely how many players are on your server and what the response time is. I've got a schedule running it against my server every ten miunutes and then outputting it to a web page that I (and other players) can check to see if anyone's playing on it.
-If you want to change some of the starting settings for your players, edit the mpnewcharacter.fl file in your EXE directory.
-If you need to move or backup your characters, don't look in the game directory, it's in your "My Documents" directory.

Questions I have:

-I've heard of a /c command line option, what does it do?
-Are there more options?
-Is there a log of INTERESTING events? Deaths, log ins/outs, level changes?
-How do the differnt chat windows work?
-Is there a way to watch ALL chat messages between players?

I would like to know if there are logs of events as well so I can write a stats results page for my server.