I run a CS server, and help admin the Thunderdome gaming servers, and I can tell you from experience that while Win may be the popular choice, it isn't the best choice. Thunderdome runs FreeBSD, and I run Linux; they are simply superior operating systems for the CS server application. Pings are lower, they are more stable, and there are more advanced tools out there for use on the linux servers.
I set up my linux CS server in very little time, and I knew absolutely nothing about the OS, I still don't really. I cant even move a file from one place to another without going into the GUI, which is easy enough to navigate and start, btw. You set up the server in the GUI, and then go to a website server.counter-strike.net that gives you a walkthrough for setting it up on both OS'es. Its simply a matter of running the hlds once you get it all in the right directories with the GUI. And NO, you never want to run it in the GUI, that defeats the purpose of using Linux in the first place.
[ October 17, 2001: Message edited by: Averron ]