I used to have a lot of projects in a single Eclipse workspace (~500), and after a certain point it became really difficult managing all of them at once. I already had them sorted into working sets but even having to constantly open/close them was a bit too much. As a result I decided to split these various projects over a few workspaces.
Now I had a new problem. All of my Mylyn Tasks (Bug Repositories/Queries) were configured for my original workspace, and that metadata was all under that workspace’s main directory (this is the default). I didn’t want to be constantly switching to my main workspace just to get bug updates, or make changes, so it’s nice that Mylyn’s data location is configurable (Window -> Preferences -> Mylyn Tasks -> Advanced).
Simply copy over your task data from $WORKSPACE/.metadata/.mylyn to some common location, and set that to be your data directory for each of your workspace preferences.