The most obvious, of course, is setting dedicated to "2", so that it reports to ID's master (bootblock will only know about servers reported to ID's master server).
Opening 29760, as Red said, is the most important part. Some more hints on the master interaction.
Your server will make an outgoing connections to port 29750 on monster.idsoftware.com (or master3.idsoftware.com - same server, Q3 "specific" name). This is hardly ever a problem, since every game browser does the same.
Also, the master will check back to your game server from port 51818 on monster.idsoftware.com, connecting to port 29760 (or whichever game port you chose) of your game server. I'm not sure how crucial it is that the master suceeds, or if the master is happy if the game server only reports the hearbeat every 5 minutes (OTOH if you change dedicated from 2 to 1 and your server stops sending the heartbeat, the master will still check back
... it happened to me once ... you have to actually stop your server for 15 minutes or so, so that the master really forgets about your server ... but this is becoming way off topic
...)