Is there a 'official' place to put PHP snippets? If I wanted all PHP removed from the front end (meaning not in views, not in the body of blocks), but someplace hidden in the background, is there a 'official' recommendation for doing so?

Drupal's framework is PHP so I figured it would have some sort of standard for this type of thing, but it doesn't appear to be the case.
I would quickly answer no to your question (and explain myself below).

The only thing that comes to my mind as a kind of answer is "place it in a hook".
But as you probably know, there are tons of these.
So, there is not one single "official" place, if I get your point right. 
Plus, using a hook means placing your PHP Snippets in files. 
Is that in agreement with your question? Or, is your question better phrased as "Is there a 'official' place in the configuration to put PHP snippets?"

Well, hope this explained the "no" answer some, if I am off, please do elaborate some more.

Cheers!

P.S.1: Sounds interesting, sounds like you have something specific in mind. :-)
P.S.2: It's worth mentioning that there are even some modules like the Computed Field that guide you (through naming conventions) to place your snippets inside specific functions.
This is similar to the hook idea, but fantastically presented and suggested in the field's configuration. 
It's one of the reasons I am so very fond of the Computed Field