Is there a good tool to compare specifically web.config files to find specifically which settings are different values and which file has settings that don't appear in both.
XML comparison should do the trick, or an XSLT might work. There must be a tool for web.config settings out there?
Use diff
It will neatly point out the exact lines and text that is different.
Diff Utilities are available for windows as well. Download here.
Wikipedia has a comparison of file comparison tools. Take your pick :o)
Use winmerge.
You should get used to version control, subversion and tortoisesvn are recommended, and ankhsvn provides svn access from Visual Studio.
In my experience, Araxis merge is the best tool for comparing any documents:
http://www.araxis.com/merge/index.html
Use it myself at work.