If it's a personal project, I say store the settings in source control. Personally, nothing kills my motivation more for a project than setting up a development environment again.
When more people are involved, I don't put these things in source control. On my team, we have a mix of IntelliJ, Sublime Text, and Eclipse being used. IDE files just add clutter, and result in pulling in commits to those files from other people for an IDE you don't use.
Also, your project shouldn't be dependent on the IDE anyway. A build server won't be booting up Eclipse to compile your product, so it should already be IDE-free. A more minor point: it eliminates personal organization within the project. For example, in IntelliJ I like to use many modules within our project. No one else using IntelliJ worries about this because we don't store the .iml (module) files.
If your team is using the same IDE then it's better, but then someone commits a bad .classpath entry because they used an absolute path. Now everyone using the IDE worries about it.
Sure, the downside is that there is more setup when someone checks out the project. I think it's worth it. We use Ivy for dependency management and have information on setup, dependencies, etc. Despite this up front cost, I think it's worth it to keep IDE settings out of source control.