Like many people, I have hundreds of fonts installed in my library. Is there any way to set fonts available on a per document basis for Adobe apps (or any other apps for that matter)?
Font managers like the two Chris mentions are really the key to this problem. They come with their own quirks and problems, but they do help.
TypeDNA is an inexpensive tool ($50 for a license for two machines). It allows you to deactivate any fonts that aren't required by the system, browse your library, make groups of fonts and activate fonts permanently or temporarily, individually or in groups. It comes with plug-ins for InDesign, Illustrator and Photoshop that allow you to access its functionality from within the applications. It can also suggest headline fonts to go with a particular text face, or vice versa, and allows filtering by font weight, width, slope (italics, for example) and "Optical size" (essentially, x-height in relation to ascender height).
Suitcase and Font Explorer similarly allow browsing, activating, deactivating and grouping fonts. Their plug-ins will automatically activate fonts used in a particular document if they aren't currently activated, but have a history of being a bit problematic with InDesign, so I'd suggest trying before you buy.
The upside of font managers is that they allow you to keep the majority of your font library inactive until you need them. The downside is that you then have an extra layer of software and an extra step to go through to find and use a font in a document.
In Indesign and Illustrator specifically, if you create a folder called "Document fonts" in the same folder as your document and place copies of your fonts there, InDesign and Illustrator will activate and use them whenever you open the document. This folder is created and populated automatically when you export an InDesign or Illustrator Package.
All of the CC 2014 design apps allow you to sync and activate Typekit fonts when you open a document if they aren't already active on your system. How font managers cope with Typekit is an open question. None of them recognize Typekit-activated fonts so far.
I'm going to second Suitcase Fusion (which is also available for Windows now). A lot has already been said so I'll just say that I've never had any problems running it alongside InDesign. I forget it's even there sometimes (as these days I tend to stick to a few sets of fonts that I always have active).
Yes it's an extra program layer, but Adobe would never put as much time into font management as these guys have.