Losing your preferences when creating a new workspace is a problem I've never quite figured out.

These days I set up a clean workspace and configure it and just make copies instead of creating the new workspaces from Eclipse.

I've heard some advocate a best practice of just using a single workspace and using views and Mylyn to manage context. But there is a point where Eclipse goes over a performance cliff with the number of files and projects and the system is just not usable. That and the ever present possibility of workspace corruption make separate workspaces the way to go for me.

Also: Key bindings suck. I used to be able to get "Home" and "End" work in a sane way on Macs, but not anymore.