I do the same, bitbucket allows you to group repo's by project or team (or both) so I always create a default docs repo.

For actual notes I just use org-mode since it can be read easily in nearly anything, supports all the bits I want and has nice html/pdf export if I need to send a todo/completed list out to anyone.

What's nice is I can keep my own meta-docs project which just links to each repo for each set of projects so I can jump around different projects transparently as well.