from the debug (in case it actually tells anyone anything...)
Loading extension: reference:file:javax.transaction_1.1.1.v201105210645.jar
eclipse.properties not found
file:/C:/eclipsex2/x2eclipse/1 not found
Time to load bundles: 10
Starting application: 1235
Don't know if this is the problem, but I was having issues with Eclipse Helios where when Eclipse was abnormally terminated, it took forever to restart. The way to get around this was to delete all the ".snap" files from the .metatdata.
Deleting the .metadata entirely is likely to lose more important project information, however. If you do that, you'll effectively have created a new workspace and you'll probably have to import the project files into it.
An IDE is no substitute for an Intelligent Developer.
Yes, the .metadata directory contains all of the information that Eclipse maintains about the workspace. If you delete it, the workspace is gone, as far as Eclipse is concerned. You can the reopen the workspace directory in Eclipse and then import existing projects.