The main reason that a virus/malware free PC that has no hardware faults slows down is loads of software running at startup and then in the background eating resources.
Your best bet would be to (if the PC is running XP).
1, Remove anything that is un-needed from the startup folder on the programs menu.
2, Use "regedit" and the search function to find all of the "run" folders and then remove anything that is un-needed from there. I have found that if you search for "runonce" and skip anything that is found in the right side of the window you will soon find the "run" folders listed in the left side of the window. If your not sure about deleting something, you can simply put a ~ (tilda) before all of the characters - this will disable the item from running, and you can simply remove it if you want it to start up later. FYI "F3" repeats the last search, it doesnt automatyically start from the top when you get to the end, you manually ahve to scroll up, and then click on "my computer" if you think you have missed something, or were just browsing as a "dummy-run" through the registry.
3, Open the "control panel", go to system > advanced > settings > advanced > virtual memory "change" button. Set it to "custom" and set the min and max to 1024MB > click the "set" button (you can select another number, 1GB is more than enough for most users, 512MB would almost certainly be fine).
4, Download and install/run "pagedefrag" and set it to run on next reboot (remember not to pounce on the keyboard when you see the blue screen apear).
http://technet.microsoft.com/en-us/sysi ... 97426.aspx
5, Delete any and all temp and temp-internet files, found in docs and setting > user name > local settings. (You can actually delete the folders). Also delete the "Temp" folder withing "Windows". These wont be visibly by default, but can easily made so within windows explorer go to Tools > folder options > view > put a "dot" in the "show hidden files and folders" option, and un-tick "hide extensions for known file types" and "hide protected operating system files".
6, Un-install any programs that never get used, or duplicate programs that sometimes occur (AOL, Acrobat reader etc, often allow you to have several versions installed side by side, yet you will only be using one of them).
7, Re-boot, watch the PC load up faster
Now run a defrag program of your choice - do NOT run more than one program, as each program moves stuff around in a different way, you will just waste time and wear out the HDD.
There are numerous other things that you can do, but these things are about the quickest easiest things to do that will have the greatest positive affect on the PC's performance.
You will need to be careful when medling with the registry. As of the moment you delete an entry its gone, and you wont be able to get it back. There is a backup option for it though, which I never use, but I would suggest you do. Highlight "My Computer" in regedit then, File > Export > Name the file > Choose where to save it.
Andy