I run a sudo gem list or gem query --local, and it only lists a portion of the gem's installed.
For instance ruby-debug is installed, I'm using it to debug stuff...but it doesn't show up in the gem list.
I've tried to run gem update —system and it doesn't do anything.
Note: if I then run a sudo gem install ruby-debug it installs successfully and is then displayed in a gem list.
This has happened to me in the past when installing rubygems via macports/apt-get and then upgrading it either manually or with update --system. You should be able to find your original list of installed gems somewhere under /opt/local; use locate to find it. You can find the new path with locate as well, but I didn't have any luck when I tried to move the them folders to the new location...so you need to manually re-install all the gems.