rails bundle clean

If you're using RVM you may use rvm gemset empty for the current gemset - this command will remove all gems installed to the current gemset (gemset itself will stay in place). Then run bundle install in order to install actual versions of gems. Also be sure that you do not delete such general gems as rake, bundler and so on during rvm gemset empty (if it is the case then install them manually via gem install prior to bundle install).

If you are using Bundler 1.1 or later you can use bundle clean, just as you imagined you could. This is redundant if you're using bundle install --path (Bundler manages the location you specified with --path, so takes responsibility for removing outdated gems), but if you've used Bundler to install the gems as system gems then bundle clean --force will delete any system gems not required by your Gemfile. Blindingly obvious caveat: don't do this if you have other apps that rely on system gems that aren't in your Gemfile!

Pat Shaughnessy has a good description of bundle clean and other new additions in bundler 1.1.

If you are using RVM you can install your gems into gemsets. That way when you want to perform a full cleanup you can simply remove the gemset, which in turn removes all the gems installed in it. Your other option is to simply uninstall your unused gems and re-run your bundle install command.

Since bundler is meant to be a project-per-project gem versioning tool it does not provide a bundle clean command. Doing so would mean the possibility of removing gems associated with other projects as well, which would not be desirable. That means that bundler is probably the wrong tool to use to manage your gem directory. My personal recommendation would be to use RVM gemsets to sandbox your gems in certain projects or ruby versions.