What are some alternatives to WinMerge and the pros and cons of each?
The best I like is Meld
There are many choices available though. As a vim fan I find myself using vimdiff, kompare for the kde crowd - there also some paid version that have linux versions like Beyond Compare . The pros/cons depends on what you're looking for/looking to do.
vimdiff is great because you can run it from a terminal, over an ssh connection, and if you already use vim, you get to keep your tools/config options.
Meld has a pretty clean user interface, and does three way and directory diffs. You'll have to try a couple and see which does the job as you're expecting them to do for your own needs.
To install Meld from the Ubuntu repos, you can run:
You can then pick the files/folders to compare, and compare them:
Another one is diffuse
It is free, crossplatform (written in python), has source code highlight, can interact with many version control tools.
Is a pretty good 3 way merge tool.
Some of its features are: