If it guesses wrong on lines that should be associated, the two (or three) files can be synchronized by marking a “common” point in the file. This can be done multiple times if necessary. I found this a “lifesaver” when comparing code written in two different but similar languages.

http://kdiff3.sourceforge.net/
from the website:
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).

Supported platforms:
GNU/Linux with KDE3,
Any Un*x that is supported by the Qt-libs from Trolltech,
MS-Windows.
Apple Mac OSX binary available.
In theory any platform for which Qt-libs work.