For some reason Eclipse decided to make it non-straightforward to uninstall plugins, there is no big button telling "Uninstall Old Software" similar to "Install New Software". Thus it becomes a bit tricky to remove installed plugins.
Open Help->Install New Software, and click on "What is already installed?" among under bunch of check-boxes below.
Select the plugins you want to uninstall from the list of software, and click "Uninstall" below. Note that Eclipse will check for dependencies in order to not delete any plugin required by another plugins to function. Thus you have to be certain that you don't have dependency issues.
Confirm the selection and uninstall, and wait for uninstall to complete.
Restart Eclipse when you are asked for it.
Almost done. The thing is what really happened was that the plugins you selected got disabled, and not actually removed from the disk. That is because Eclipse is really strong about not removing, but disabling their plugins as stated in Eclipse FAQ.
If you want to remove plugins from disk, you will have to go to "Installation History" tab, after opening Help->Install New Software, and then delete a plugin configuration that contained unnecessary plugins.
In "Installation History" tab you can also revert installation configurations, however once they are removed, they are unrecoverable.
These instructions work for Eclipse Helios 3.6 Release 2, things can (and probably will) be different in future versions.