Sophos Security Guide

Got this url http://www.sophos.com/security/analyses/index_st_controlled_application.html

That list the popular applications and their common or interesting threats.

AIM
Ares
AudioGalaxy Satellite
BearShare
BitComet
BitSpirit
BitTornado
BitTorrent Mainline
BOINC Client
eDonkey2000
eMule
FileTopia
Folding@Home
Gaim
Google Talk
Grokster
 ICQ
iMesh
JAJC
KaZaA
MLDonkey
Morpheus
MSN Messenger
Net2Phone
OverNet
Shareaza
ShareP2P
Skype
UD Agent
Windows Live Messenger
Yahoo! Messenger