These are tools that I use on a regular basis. This is not meant or implied to be an endorsement. Nor should the fact that tool not be listed be construed as anything significant. The latter simply means that I've not used the tool or I use another tool already that does the same thing.
In any instance, use these tools with extreme care. Any misuse, either accidental or otherwise can cause major issues.

Note that due to the nature of some of the more specialized tools, some of these links are likely to become invalid rather rapidly. Site contents are subject to change on a very regular basis and typically will be expanding.

Online scanning tools

http://www.kaspersky.com/virusscannerKaspersky online scanner links. One will do a system scan and another allows select file(s) to be scanned. Crapware removal must be done manually however.
http://housecall.trendmicro.com/Trend Micro online scanner
Panda online scanPanda Software online scan

Local scanning tools.

http://www.kaspersky.comKaspersky anti-virus. Has an option, that when enabled, makes it rather aggressive towards crapware.
http://www.lavasoftusa.comHome of Ad-Aware SE.
http://www.spybot.info/en/index.htmlHome of SpyBot
http://www.nu2.nu/pebuilderBart's PE. Using this tool requires a great deal of knowledge to use effectively.
http://www.majorgeeks.com/HijackThis_d3155.htmlHiJackThis download from MajorGeeks
http://www.majorgeeks.com/SpywareBlaster_d2859.htmlSpyware Blaster - prevention rather than cure
SyscleanStand alone antivirus scanner from TrendMicro
http://www.silentrunners.orgSilent runners - an alternate startup scanning tool
KillboxThis tool allows, among other things, the ability to delete at reboot
http://www.cexx.org/lspfix.htmWindows 9x/Me oriented tool for correcting Winsock issues. Note that it will work on NT kernels (that also means XP)
WinSock XP FixXP Specific Winsock repair tool; NOTE that as of XP SP2, the system has an integrated tool for reseting the TCP stack; "netsh winsock reset"
SysinternalsA variety of tools are available here; Regmon, Filemon, Process explorer, Autoruns and a plethora of other handy tools. Note that these tools typically require a good deal of knowledge in order to use effectively

Highly specialized tools. Use with extreme care since false detection is not unusual and taking action on the wrong thing can be harmful.

http://skads.org/special/rkfiles.zipAnother Qoologic tool

McAfee and Symantec removal tools. I've added these here since typically a client running either of these products that has been compromised can not otherwise gracefully uninstall Symantec or McAfee. And typically they must be uninstalled before it's possible to actually gain control of the machine.

McAfee Removal toolMcAfee product removal
Symantec Removal toolSymantec/Norton removal tool