Where can one find a list of deprecated methods, APIs, etc, in order to upgrade from Rails 2.x to Rails 3?
I don't think you'll find an exhaustive list of depreciations because it really depends on what version of rails you are upgrading from. For instance, Rails 2.3.9 (just released) added additional depreciations over the previous release.
The Rails Upgrade Handbook (as mentioned above) is a great tool and contains 12 pages of depreciation warnings and how to fix them. I don't think they'll be published here because you should just drop the $9 and download the pdf to get the list. The included tutorials and other information makes it well worth it. It was for me.
If you don't want to pay for good information then just run the rails_upgrade plugin for your specific application. More information on how the plugin is on the rails upgrade plugin github page.