Use .NET Reflector (Free version is all you need) to open the dlls then right-click and choose to export them to separate directories.
Then use ExamDiff Pro to compare the directories (You can get a 30-Day free trial). You can navigate through the sub folders and open each file as necessary into a new Comparison window (Just double-click in the ExamDiff Pro Window). Works awesome!
ExamDiff Pro also has a Dump PE32 plugin that will do a comparison directly between .dll and .exe files. This is helpful to look at header changes and flags binary differences, but will not decompile it for you (so use the Reflector method above).
