One tool I’m always using is Beyond Compare.  This is one of those ‘what did I do before I discovered this’ tools.  Folder compare, remote compare over FTP, merge, etc.  All the good stuff you expect in a diff tool.   I’ve been using the 2.x version forever and kind of gave up on checking their site for updates but a few days ago I checked and WHOA – version 3.0 is on the way (in beta) AND…

They have a Linux version! Holy S–T Batman!!!

I haven’t given it a really thorough test but all the basics seem to work just as well as the Windows version.  They also have a nice upgrade plan and you can by a ‘dual platform’ license that covers both Windows and Linux versions.  Best thing is it’s still under $50 for the basic version. Pro adds a few things like 3-way merge, SFTP support, and a few other features.