There is no GUI client for linux, but there are programs unrelated to folding that display moecules with lots of pretty colors. I'll post back when I can remember the name of one of these.
About the clients- I usually run the clients as a background service, thus invisible, and have them start at boot-time automatically. Some simple shell scripts make it easy to start/stop/change user/or view the status of my clients.
Client type- There are two clients to use for linux that are fast- 3.24 "B" which works with distros that have a newer glibc installed (redhat 9, mandrake 9.x, among some others), though 3.24 doesn't always do SSE very well on every WU with AMD machines. The other is 3.25 beta, which works on most distros except the newest releases. This one does SSE better with AMD's. Both of these clients are as fast as the windows client or very, very close.
You can also fold with the windows client if you use wine. This is not very difficult for most distors. Redhat stopped officially supporting wine as of version 9, though with some tinkering, you can get it installed.
If you have a windows machine on your network, you can configure samba so that parts of your linux filesystem are shared across the network. That way, apllications like EM3 can read the progress of your linux machine(s) (and you can also transfer files between your linux and windows machines). There are also some programs similar to EM3 that work in linux. KDfold and foldmonitor come to mind, though I think KDfold will require old libraries to be installed if you run it on a newer distro.