How can I integrate Homebrew with non-managed software in /usr/local?
I use 1.

I just compile my software using /usr/local as the prefix and I'm done. I had no problem so far. I don't know whether I'll experience problems, but I started ~1y ago and so far so good. 

However…

If I'd have to start again today, I'd follow 2 (which I didn't know at the time). That way it's easy enough to know where everything is and what, exactly, the software has installed (since the hierarchy for /usr/local/Cellar/foo/1.0 is something like

bin/      etc/      include/  lib/      share/


)

3 doesn't seem worth.