Winmerge: a sweet application with great keyboard shortcuts to let you compare and file differences and merge them. Allows merging into existing file but is only for Windows (well I guess you could guess that from the name). KDiff3 is a good alternative with cross platform support (Windows, Linux, Mac, Un*x) but when saving the merged file it prompted to save as a new file not an existing file. I had over 50 files to merge today so I didn’t want to manually file each file and save them individually.