AutoRuns - This free program finds all of the hidden auto-start entries on your computer and provides an easy way to disable them. This is a very powerful program and should be used judiciously by inexperienced users. (XP/Vista 32/64bit)
Partition Logic - Disk partitioning tool which allows you to change partition sizes, create new partitions, combine partitions and other useful functions. (XP/Vista 32/64bit)
Process Lasso - An interesting free program which throttles CPU hogging programs to increase system responsiveness. I would reserve use of this program to low end systems. (XP/Vista 32/64bit)
RegCool Registry Editor - The best free registry editor I've used. Great interface and search utility that displays all results at once. (XP/Vista 32bit)
Startup.cpl Startup Manager - Adds a "Startup" icon to the Control Panel. This shows what programs start with Windows, where they are starting from, and allows you to easily prevent them from starting. (2000/XP 32bit)
Startup Inspector - Provides information about startup applications. Startup Inspector includes a database of popular programs and provides information including: if the program is required, and if there are any caveats to disabling the program. (XP/Vista)
UpdateStar - Monitors your freeware, shareware, and commercial software for updates. The programs database is maintained by the users, with over 80,000 programs currently listed. (XP/Vista)