Alternative for WinMerge in Ubuntu

Meld (alternative link)

Meld is a visual diff and merge tool. You can compare two or three files and edit them in place (diffs update dynamically). You can compare two or three folders and launch file comparisons. You can browse and view a working copy from popular version control systems such such as CVS, Subversion, Bazaar-ng and Mercurial. Look at the screenshots page for more detailed features.

I like diffuse:

Diffuse is a graphical tool for merging and comparing text files. Diffuse is able to compare an arbitrary number of files side-by-side and gives users the ability to manually adjust line-matching and directly edit files. Diffuse can also retrieve revisions of files from Bazaar, CVS, Darcs, Git, Mercurial, Monotone, Subversion, and SVK repositories for comparison and merging.

gvimdiff is handy for quick comparisons. Install gvim to get it.