I'm right there with you Q.
Although the "majority" of edits I've made to the core files (excluding sign-up and login) have been so that the primary domain could be a sub-domain, and the sites when created could be on the same level subdomain.
It hasn't been much, surprisingly. Only a few minor edits to a couple functions in wpmu-functions, and then sign-up.
Of course I've also added a captcha to the sign-up process, as well as a registration agreement that has to be checked in order to sign up.
I did keep track of most of my changes, at least in the core files, so when it's time to upgrade I can compare what's changed in the files I've modded.