The broad-sword swing is to go to the "Project" menu, then "Delete Unused" and select "Materials..."
That will nuke all materials that are not used in a current scene.
The other way is to go through every scene to determine which materials are being used for what (if you click on an object, it will show you which materials are applied to which faces in the material manager), then only keep what you need. Fonts are MUCH more difficult to do, but it's a similar process. Each piece of the font (face, stroke, shadow, etc) has its own material, and there's no "font material manager," making that pretty chaotic in there. I just finished cleaning up 240 scenes worth of fonts, and it was nuts.
#XPression