An article was written by the Christian Apologetics & Research Ministry (CARM) on just this subject. Using data from Charles Phillips & Alan Axelrod’s three-volume book The Encyclopedia of Wars, the author of The Irrational Atheist (Vox Day) has determined that only 6.98% of all wars were religious or faith-based (this percentage is for all world religions/faiths). Islam was the most warring, and when you subtract their percentage from the above one, that only leaves 3.23% for the rest!!
Here is a rough pie chart of the compiled information:
(Source: CARM, http://carm.org/religion-cause-war, Compiled by Vox Day, Data taken from The Encyclopedia of Wars)
If you want to read more on this, check here:
1) http://carm.org/religion-cause-war (Originally where I found the article)
(Where CARM found their material, pages 104-106)
3) http://books.google.com/books?id=1ghxQgAACAAJ (Where Vox Day found his data)