Just installed v3.0-alpha with Multi-Site "Network" enabled (fresh copy, not upgrade). Everything is working fine.
I have noticed one issue:
Super User > Sites > (choose site) > Backend
This link does *not* appear to be dynamic/related to the specific site. For example, if you had 3 sites:
The link for all of them would be "mysite.com/wp-admin/"
I assumed this was intended for some reason, but then realized that this definitely had a static functionality (it was the default page administration only, not the particular blog selected).