First, you should update your gems, so you have newer versions for all the gems you're about to remove. While you're at it, update rubygems as well.
sudo gem update --systemsudo gem update
Now blast the directory containing the gems that came with OSX.
sudo rm -r /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8
If, for some reason, that directory does not exist on your system, you can see rubygems stores its gems by running gem env paths. Most likely, the old gems have already been cleaned.
Enjoy being able to clean up all the old gems on your system.
sudo gem clean
Removing the gems this way is permanent. If you don't like that thought, rename the 1.8 directory to 1.8.dead, and create an empty 1.8. This way, rubygems doesn't see the old gems, but they are still around, if you need them for some reason. So, instead of rming,
sudo mv /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8 /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8.dead
sudo mkdir /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8
The pre-installed gems have been released 2 years ago, so they're really old by now. They need to go away. Doing a gem clean will fail to remove them. (tested with Rubygems 1.3.1 and below) What's worse, gem clean will fail to remove other old gems that you have installed so, after a while, you'll have a lot of cruft on your system.
I wrote this post because, up until now, I've been too lazy to figure out the gem cleanup situation. Now that I finally did, I want to make it easy for others to get their systems clean.
I've described a quick way to remove the old ruby gems that come preinstalled with OSX Leopard. This is useful because gem clean is non-functional in the presence of those gems. I hope you have found the post useful. Please comment if you have better or quicker solutions to this problem.