Yeah you need to keep the fonts out of your System Library if at all possible.
Mine only contain the base fonts that Macs ship with since the system uses some for display.
The system and any open apps need to account for any fonts in the system library as they are always considered active. If you launch illustrator and watch the splash screen in the lower left you'll see it loading plug ins and fonts.
The more fonts in the System Library the longer it takes and the pokier everything runs.
I have a •Fonts• folder right in my home folder and everything is in alphabetized sub folders.
I added that whole folder to Font Xplorer. There are plug ins that can be enabled to auto activate for most apps so it does a lot of stuff on its own.
Just to view and print try Fontcat, 30 day trial then $20.
http://www.pure-mac.com/downloads/fontcatdl.html
Or more basic FontBook 4.5, shareware that watermarks pages but I don't think you care about that, $10 to remove watermark
http://www.lemkesoft.org/files/fontbook/fontbook45ub.dmg