Guillaume,
I believe there are some plugins in each release that maintain their old version numbers when they don’t change (like some of the connectors), if this is what you are seeing then it is normal. However if you are seeing multiple copies of plugins, for example 2 or 3 Tomcat 5 connector plugins all with different versions then do the following:
If the directory you installed the new version of MyEclipse to is different than the old directory (e.g. C:\MyEclipse-3.8.2 and C:\MyEclipse-3.8.3) then you can navigate to Help > Soft Updates > Manage Config, find the extension that points to the C:\MyEclipse-3.8.2 install, right click -> Disable it, hit “No” for restart, shut down Eclipse, and go erase that old MyEclipse directory.
If you installed it to the same dir as the old one (C:\MyEclipse) then there isn’t anything you can do short of manually cleaning out the dirs, but the good news is that Eclipse is smart enough to just load the newest instance of each plugin, so having many copies is relatively harmless.