Well, unfortunately WinME is notorious for problems. This may be beyond your scope, but I'd flush, format and install WinXP, preferably Pro.
Aside from that, go to the 'start' button, type in Msconfig and click Run button. Then take a look at the Startup tab and see what programs are automatically starting when you boot up. There may be some things that should be turned off. I would turn off everything but Systray and Explorer and see how it runs. Then selectively add the valid startup programs back one at a time.
Is there any pattern to what activities are occuring on the pc when it freezes? For instance, does it always happen while on the internet, or something?
You might also check cnet or similar site for utilities that check the registry for bad entries again but sounds like you did that to fix the original problem.
Have you re-applied any Windows ME updates since reinstalling? If not, I'd go to Microsoft and do that next.
Also, doubtful that this is it or that you haven't already checked, but if not, check your Temporary Internet files. Is the number of items high? If so, delete them and see if that helps. There's also an option in the 'advanced' part of Internet Options that will automatically delete those temp files whenever you close the IE browser window.
Hope this helps a little.