linux as an alternative? I'd say windows is the alternative. Linux/BSD dominate by far the number of server on the net,
http://news.netcraft.com/archives/we...er_survey.html you can see apache is running more than 2x Microsofts IIS (not to say people cant run apache on windows). Also with Samba 3 coming out benchmarks i've seen show it can handle more connections and serve files faster than windows 2003 server.
Now that that little rant is out of the way

i dont know of any books that deal with comparing the 2 OS's and dont see why anyone would publish a book on that subject since things change so quickly. The best thing to look at published documents on the net from garner or other research companies. A topic you might want to cover is the total cost of ownership (TCO) for windows vs. linux servers.
http://www.google.com/search?hl=en&l...=Google+Search is a good start.
Try to get past what the articals say and find the original published papers.