It can be as simple as using the built-in "Disk Cleanup" and "Disk Defragmenter" Utilities already available in Windows ( Start - All Programs - Accessories - System Tools )
HINT: You SHOULD use BOTH but start Disk Cleanup first !
Of course, sometimes it needs the BIG cleanup and here is my technique on how to do a TOTAL non-destructive cleanup: a few tricks (and associated free programs) I use when helping friends with problems.
1) The Java Runtime Environment causes issues, you should use a free program I use myself called JavaRa to get the latest JRE and remove older versions. This will ensure the security of your computer and a little extra space on your hard disk. Find more information here: http://raproducts.org/javara.html and the download link here: http://raproducts.org/ ( Currently, JavaRa supports Windows Vista without UAC so if you have Vista and are not comfortable temporarily disabling it, don't use JavaRa )
2) Flush every single possible accumulated browsing junk in ALL your browsers (you should always delete these from time to time).
Method One (now): In Internet Explorer, click the Tools menu, then Delete Browsing History and in the box, click the Delete all button (bottom left) and Yes.
In Firefox, go to tools, clear private data, make sure all boxes are checked and then click on the clear private data now button.
Method Two (in the future - about every two weeks for normal use of the internet - every week for heavy use):
In Internet Explorer, click the Tools menu, then click Delete Browsing History and in the box that opens, do the following steps (in order)
1) click the button near Temporary Internet Files, click Yes and wait for the box that opens to close.
2) click the button near History, click Yes and wait for the box that opens to close.
Finally, click the close button (bottom right) to finish.
In Firefox, Go to tools, clear private data and uncheck all except Browsing History, Cache and Authenticated Sessions boxes and then click on the clear private data now button.
Note: Close your browser ( This is good for Internet Explorer and Firefox ) when you're done to clear cookies that are still in memory.
For older versions of the same programs or for other browsers, check their help files for guidance on doing the cleanup.
3) Turn off the restore point utility.
Here is a guide for XP: http://support.microsoft.com/kb/310405 and an article for Vista: http://windowshelp.microsoft.com/Windows/en-US/Help/9f6d755a-74bb-4a7d-a625-d762dd8e79e51033.mspx
4) Install a free cleaner called Glary Utilities ( http://www.glaryutilities.com/gu.html ) to remove Windows junk files, registry orphans and/or remnants of installs/uninstalls (there is always some).
5) Defragment your drive with your defragmenter.
6) Turn system restore back on. ( the same guide and article given in part 3 )
( A word of caution, with programs this powerful, be sure to read all instructions and help files completely so that you apply fixes correctly the first time ! )
NOTE: Finish by making sure to download and install the very latest stable drivers for EVERYTHING and that they are for the correct OS (Don't use XP drivers on Vista and Vice versa - one exception would be if they are indicated for both OS) for a better overall computing experience.
Hope this helps