I have both the Peterson and Thayer's. Most of the time I turn to the Thayer's first, although I do use both. Thayer's operates more smoothly, has more information, and has much interesting and flexible quizzes. If you also own the Thayer's Birder's Diary(v.2), then you can develop customized quizzes as well. Basically, in my opinion, the Peterson is simply the fieldguide plus bird songs in one package. The strength of the Peterson is the same as with the fieldguide: the illustrations. Thayer's uses photographs which I don't find always work for identification purposes.
There are some comparisons of the three programs at the Thayer's website that are fairly objective.
http://www.birding.com
Cheers
Gail Spitler
Johnsons Landing, BC
gspitler at awinc.com