Scan again using ad-aware and spybot to confirm that the machine is relatively clean. Then run CCleaner. After that, let Erunt and NTRegopt look at the registry. All these tools are safe and useful.
Also, let Trend Micro's Housecall scan your system, it's pretty good at picking up stuff. You can get a free scan at the website.
Incidentally, after booting and with the computer sitting idle, how much CPU is it using and what application is using it? Ideally, CPU should be around 10% on an idle computer and the main process should be System Idle Process at 90% or higher.
If you don't routinely use Start -> Search to look for stuff within files, turn of Microsoft's indexing service. That can bring some systems to their knees.
After that, if there's no improvement, then we need to dig deeper :-)