kdiff3

KDiff3 is a program that:

compares or merges two or three text input files or directories,
shows the differences line by line and character by character (!),
provides an automatic merge-facility and
an integrated editor for comfortable solving of merge-conflicts,
supports Unicode, UTF-8 and other codecs, autodetection via byte-order-mark "BOM"
supports KIO on KDE (allows accessing ftp, sftp, fish, smb etc.),
Printing of differences,
Manual alignment of lines,
Automatic merging of version control history (Log),
and has an intuitive graphical user interface.
Windows-Explorer integration Diff-Ext-for-KDiff3 - shell extension included in installer (originally by Sergey Zorin: see also Diff Ext)
KDE-Konqueror service menu plugin
Simplified integration with IBM-Rational-Clearcase for Windows (Details).
Read what else is special in a short abstract (PDF).