I'm going to take a leap here and guess that you haven't used any sensible version numbering. Definitely take Richard MacCutchan's advice and use proper version control - there are plenty out there.
If you want to determine the disassembled contents of the different executables you can use the
ildasm[
^] tool that comes with Visual Studio.
If you need to compare the outputs from different versions of the exe then get a text comparison tool e.g.
http://winmerge.org/[
^] (free).