Ruby-gems is used to install rails/mongrel and their dependencies. Portage does not recognize that, and wants to install mongrel and its dependencies when installing the new amarok for example.
Steps to Reproduce:
1. emerge rubygems
2. gem-install mongrel
3. emerge --sync
4. emerge -pv amarok
Amarok still wants to emerge mongrel.
I'm not sure if this should be a bug, but I know that myself and alot of other people use gems to maintain our Rails application and dependencies, having to use the portage versions of these applications becomes troublesome...
Sorry, there's no way for portage to know about stuff installed by third-party tools, and there won't be any unless someone writes a g-cpan like tool for ruby gems stuff to install such stuff from ebuilds created by the tool.
There's also not much of a reason to use gems for stuff that actually *is* in the official tree. If you really must, that's what package.provided is for (see man portage).