Eclipse itself will be installed where you've unzipped the file you've downloaded. This directory contains Eclipse.app
, configuration/
, plugins/
and features/
(amongst others).
Your workspace/
directory (in your home directory by default) contains all your projects and various settings too, in workspace/.metadata/
(see dot files if you want to have a look). Deleting the workspace will delete your own project files of course, so you would need to make sure you have a way to restore them from a clean version (for example from a version control system if you're using one).
If you don't want to delete your entire workspace, it might be worth moving it away and then copying the projects back in, leaving the new workspace/.metadata/
clean, to see if this fixes your problem.