Here's my list from my security toolkit. These are all Windows-based. I'm continually adding to it but here's current state today.


TOOLS:

SpyBot Search & Destroy [installer]
Adaware SE Personal edition [installer]
CWShredder
HijackThis [standalone]
BHODemon
SpywareBlaster [installer]
SpywareGuard [installer]
Windows 2000 Resource Kit Utilities [standalone]
MD5SUM for Windows [standalone]
ZoneAlarm free [installer]
PasswordSafe [standalone]
ScripTrap
Etheral [installer]
Winpcap [installer]
SuperScan [standalone]
WotWeb [standalone]
OpenPorts [standalone]
TCPView [standalone]
TDIMon
PortExporer-byDiamondCS [installer]
PrcView [standalone]
ProcessExplorer-SysInt [installer]
PSKILL by SystemInternals [standalone]
PSLIST by SystemInternals [standalone]
iehistory-gui [standalone]
Trojan Defense Suite (TDS3) [installer]
WGET [standalone]
Curl [standalone]
Achilles [standalone]
NTLAST [standalone]
Founstone toolkit [standalone]
WinPatrol [installer]
NetCat [standalone]
PSEXEC [standalone]
VNC Server [installer]
VNC Viewers (UltraVNC, TridiaVNC, RealVNC) [standalone]
Shed [standalone]
Netstumbler [installer]
AVG Free anti-virus [installer]
CookieView [standalone]
Pasco [standalone]
Knoppix LIVE CDs (separate CDs): Knoppix original, Helix, Penguin Sleuth Kit, Phlak, Live Defender


REFERENCES:

List of security websites
Startup-Apps-LIST-by-sysinfo-org_files (process reference)
Task-List-Programs-by-answersthatwork_files (process reference)


Let me know if need more info about these.