As I said, I hop back and forth between GUI and command line; I haven't personally needed to deal with a folder diff with 1000+ files with one line changed each

As I said, I hop back and forth between GUI and command line; I haven't personally needed to deal with a folder diff with 1000+ files with one line changed each, but if I did, command line seems like a reasonable option. Beyond Compare (linked above) lets you set patterns to ignore, which has been incredibly useful for when an autogenerated time/date stamp is changed in 1000+ files; I can say "ignore that change; tell me what changed that DOESN'T match the pattern". You can do the same thing with grep on the command line of course. But then you lose out on all the GUI awesomeness. I've used Araxis, and it's Even More Awesome, but 5x the cost (last I checked) as Beyond Compare, and I didn't think it was 5x as awesome. BC has gotten much cooler since then too (with comparison plug-ins, and bitmap compare -- let's see diff compare two bitmaps and tell me which pixels have changed! -- and DOC file compare, and normalized XML file compare, and so on ;).