I had an interesting problem today.

Flex Builder 2 crashed while I was working on one of my projects using a custom workspace. Flex Builder will start then stop with an error to go look at the .log file in your .metadata directory in your workspace.

There is a handy .metadata directory with a .log file in it and it gives you all kinds of information about the problem. (this is an eclipse structure; I believe).
In this .log file I found an error:
!ENTRY org.eclipse.core.resources 2 10035 2007-05-24 19:44:08.812
!MESSAGE A workspace crash was detected. The previous session did not exit normally.

Now to solve the issue:
With a little luck and some guess work, I found that you can go to the directory for your workbench config files and fix the problem.
[workspace dir]\.metadata\.plugins\org.eclipse.ui.workbench

In this directory you will find a file called workbench.xml
Rename it to something else (because I like backups), then start Flex Builder again.
You should be able to open the workspace without a problem.

Good Luck!