To robbier & edpaffjr
I realizw this is a difficult thing and I am not in your situation.
Mercury Mail and Filezilla probably could be preserved intact, merely by backing them up or copying to a secure location. XAMPP does not do anything with the Windows registry, so you should be able to put them right back in place, You would of course be wise to get familar with which files the configuraions are stored in,
As for the messy stuff - getting all the differences in configuration files for PHP and Apache, I can tell you a solution (and its free and very straightforward) I use it to anaylyze my installations and code, and find out where I lose track of little changes. (note you would have to save your old XAMPP intact elsewhere, like a renamed folder for this to work)
WinMerge. Its a graphical 'diff' on steriods, let's you compare individual files or whole folder hierarchies.http://winmerge.org/
YAY! Winmerge! I don't have the time or resources to maintain a formal devlopment system like subversion, but this gem solves those 'why does this work and that doesn't' questions about my HTML, PHP, CSS and Perl code.