Assuming you do not use Maven, then you should definitely check in versions of 3rd party jars. You (or more importantly, the maintenance developer coming along after you) should be able to pull a version of your application from the repository and have all the correct versions of all the 3rd party jars required at compile- and runtime.
You also should maintain the versioning history of the 3rd party jars, again to help the maintenance developer out. Checking them in to the repository is the easiest and most effective way to do this.