Here is the list of the BEST comparison software for various types of projects (according to our research):

For professional developers:

Three-way comparison

Araxis Merge
Guiffy 8.0
ECMerge Pro 2.0 - Buy with 15$ discount!
UltraCompare

Two-way comparison

Beyond Compare 2
ExamDiff Pro

For document comparison:

Compare Suite - Buy with 15$ discount!
Compare PDF
Compare Spreadsheets
CSDiff (free)

For HTML/XML comparison:

Araxis Merge
Guiffy 8.0
HTMLDiff
ECMerge Pro 2.0 - Buy with 15$ discount
Beyond Compare 2
ExamDiff Pro
UltraCompare

For binary files comparison:

Araxis Merge
ExamDiff Pro

Outstanding visual image comparison:
ECMerge Pro 2.0 - Buy with 15$ discount!

Beyond Compare 2
UltraCompare
Compare Suite - Buy with 15$ discount!

For folder synchronization:

Araxis Merge
Guiffy 8.0
ECMerge Pro 2.0 - Buy with 15$ discount!

Outstanding archive comparison:
Directory Toolkit

Heatsoft ADCS 1.20
ViceVersa Plus
Foldermatch - Buy with 10$ discount!

For version control integration:

Guiffy 8.0 for CVS, Tortoise, Subversion integration, for CM systems integration
WinMerge for CVS integration (free)
Synchronize It! - Buy with discount! - for folder synchronization projects

For occasional comparison tasks:

IsEqual - Buy with 15$ discount!