Slow responding PC

I have a Windows 2000 pc with a 1.2Ghz processor and 256Mb ram. It also has a 60 gig Western Digital drive that has been partitioned into 3 varying size partitions. The problem I’m running into is that initially when I built this system it would access programs quickly. Now it seems when I click on a program I wait a few seconds before the programs opens and starts running. This sluggishness caused me to check to see if there was any viruses on my system but my McAfee is at the latest virus definitions and a virus scan did not reveal anything. I also have ran Adware to remove any lingering spyware yet the sluggishness persist. Will the ATA settings or Bios settings make a difference in the speed? Any ideas why?