A "fix" has been offered for making Twitter Tools work with the new Twitter restrictions; you essentially have to register your site as a Twitter app. It's a bit convoluted to set up, but it does work.
However, there's a problem with the fix for sites running Multiuser. The information you enter about your twitter app gets assigned to the entire Multi-site. I went through the "fixing" process on one of my sites and it worked - I went to do the same on another of the sites, and it had the info I'd already entered the first time.
This means that only one site on my multi-site install can forward posts as tweets to Twitter. I'm kind of at a loss for what to do to rectify this. Does anyone have any suggestions?