Your post was a bit brief, so forgive me if these seem obvious. Virus scanning and protection up to date? Have you deleted unwanted programs in "startup" in the "msconfig" file? If you don't know about this one, do a search on this site. Made a huge difference to my system.
My installation of win2000 went well and I chose not to 'upgrade' the file system to NTFS from Fat32, the system has been slowing over time and starting to get flaky, as you describe. The only problem I have, is I don't know how to upgrade the Fat32 to NTFS now I have installed win2000. Wish I did?