I mentioned this on IRC previously but I decided I would address it here as well.
There is a client/server project that has been consistently under active development for some time now known as R1Q2. From what I have seen this flavor of q2 has a really solid goal in providing security and performance enhancements from 3.21 as well as providing some really great features to the server admins. I am hoping that maybe we can learn some lessons from this project and make some of the enhancements that are offered in r1q2 available for server administrators using the dp alpha releases to run servers.
In the mean time I'm going to start running a few different configurations of the server on linux and windows environments to be able to provide any advise or assistance to anyone who would like to start using this dedicated server over ncserver, a quiake2-3.21 or the pb2 standalone binary.
Edit: Sorry forgot to post link -
http://www.r1ch.net/stuff/r1q2/