In most cases, I think you are going to find that you will be running a tracker on a Linux box versus a Windows box. Most likely it is cheaper, and will be the option that you'll end up picking.
The only thing that comes with this, is there can be a learning curve. We had the option of picking either a windows box, or between various linux distros. In the end, we chose Ubuntu. I had some experience with using Ubuntu, and it is known as being a very friendly Linux OS.
Ubuntu also has just tons of documentation, guides, tutorials, and forums that you can read up on. Going into this, I only had experience with messing around on an Ubuntu machine, but only the desktop version. I've never used the server version.
The biggest "shock" to me was, "Wow. It really is only command line". At first, this was the hardest part for me. I felt more comfortable doing some of the finer tweaking of the server when using a gui, and I didn't have that option. However, it really was a blessing in disguise.
All I have to say is just give it a shot. When you want to learn how to install an application, look it up. How to configure a service? Look it up. In the end, it really helped me more fully understand the Operating System, and make me feel much more comfortable operating everything from the command line. When I had to do things that I didn't know how to do (which was nearly everything) I just looked up and followed a guide.
While it might be a slow start, you'll gain some very valuable knowledge doing it this way. Unless you are pretty knowledgeable with another distro, I'd recommend using Ubuntu as your main OS.
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