Managing multiple eclipse configurations
Gene De Lisa
Introduction
The built in Eclipse update manager is great. Unless you need to work with multiple versions of different sets of plugins. Or if you move from one version of Eclipse to another you want your plugins to move with you. If you installed them under the Eclipse installation directory you will have a tough time.
Links
If you have used WSAD, RAD, MyEclipse or other Eclipse based IDEs (i.e. sets of plugins) you may have noticed that they created a directory named links under your Eclipse installation.
RAD link Directory

Each file that has the .link extension contains a line that points to the plugin directory. For example the first RAD link looks like this;
path=C:/Program Files/IBM/Rational/SDP/6.0/csdev
Your plugins
I download each plugin to a decidated directory. I then unzip them with a descriptive name. Unfortunately some plugin zips come with the instructions "unzip to your eclipse plugins directory". This puts the package directories (e.g. com.bozosoft.coolplugin) into this plugin directory. If you unzip them else where you may need to create an empty directory named eclipse. The path specified in the link file must be the parent directory of a directory named eclipse. Notice that in my custom plugin directory that under each plugin directory there is an eclipse directory and the plugin files are under eclipse.
My custom plugin directory looks like this:
My Plugin Directory

Caveats
Check your plugin by looking at Help->About Product (Product might be Eclipse or RAD etc). There is a plugin button where you can check to see if you were successful.
The updates you make are stored in your eclipse directory in this directory:
C:\eclipse-SDK-3.1.2-win32\eclipse\configuration\org.eclipse.update
There doesn't seem to be any way to remove an update site once it has been added with a link file except for deleting this directory. Someone correct me if I'm wrong!
Managing sets of links
In my eclipse plugins directory I make sets of links in separate directories. For example, the Web Tools Project along with Hibernate tools. I wrote simple batch files or shell scripts to remove and update the links in the eclipse/links directory and copy the chosen set there.
Caveats
It is possible that you have older cruft still mixed in to your configuration. Try running eclipse with the -clean flag.