Flickr has a blog post on how they plan to keep the commons with their new limits on free accounts.
1. Flickr Commons partnership with NASA, Smithsonian, etc are staying.
2. All Creative Commons licensed photos uploaded & licensed before Nov. 1 are staying, even on free accounts with more than 1000 photos. (Further uploads will be limited until they either buy a Pro account or drop below 1000)
3. Non-profits can apply for free, unlimited accounts.