I've been using Eclipse for my CF development for several months now, and I found an article awhile back that explains how to set up Eclipse so it's easy to run multiple versions, as well as keep all of your plugins in one place. This method has been working very well for me, so I wanted to post a link to the article in question:
Managing Multiple Eclipse Installations - by R.J. Lorimer
I encountered one issue with this method when I upgraded to Eclipse 3.4, so I thought I'd post the solution here.
The problem is that you need to have access to the menu item Help -> Software Updates -> Manage Configuration... to tell Eclipse where to find your plugins. I'm sure you could specify this in some XML file somewhere, without going through the UI, but I don't know where that is. Anyway, that menu item is absent from the standard Eclipse 3.4 menu, but it can be resurrected.
Just go to Preferences -> General -> Capabilities, and check "Classic Update". Voila - Help -> Software Updates -> Manage Configuration... is back!