Computer Running Extremely Slow?

I have an Acer Inspire 5736Z laptop which I mostly use for browsing the internet and playing some games. It still has 100gb free on the hard drive, and 3gb of ram. I have had it about 10 months. Yesterday a game I was playing crashed, and around the same time a Spybot pop-up appeared which said:

Category: Session manager
Change: Value deleted
Entry: BootExecute
Old data: autocheck autochk *
New data: [greyed out]

I was unable to click Allow Change or Deny Change because the laptop had frozen. I waited several minutes and tried to shut the game down using Task Manager processes, but nothing worked. In the end I shut it down by holding down the power button.When I restarted the laptop was going extremely slowly. I'm talking 5-10 minutes to open a blank Notepad. I don't know if it's to do with the Spybot message or if I damaged something by restarting in that way.This is what I have done so far. It is all guesswork on my part so I don't know if it was pointless:

- Started in safe mode. Everything runs very quickly. I started up my usual background programs one by one: Avast, Spybot, ZoneAlarm, iTunes, Audible download manager and OpenOffice. It still ran quickly.

- Ran CCleaner and deleted unncessary files, but it only amounted to about 400mb.

- Performed an Avast scan. Came up clean.

- Performed a Spybot scan. It reached the end and then froze before showing the results.

- Tried to use Spyboy's recovery but I think the CCleaner deleted those files because there was no recovery data :/

- Uninstalled the game that crashed, and other programs that I no longer use.

- Started again in normal mode, still going painfully slow there.