One of the most noticeable advances was the inclusion of 'tabbed' browsing for your e-mail client. The popular tabbed style was grabbed straight out of the Firefox play book, and works quite well with Thunderbird. Tabbed browsing allows you to open multiple folders in your email client, and you can view your e-mails in an almost web browser like fashion.
To me it begs the question: Will Thunderbird and Firefox meld into one application? Why not integrate the two so that they are one in the same application? If Google can base and entire operating system on a web browser as they are with Chrome OS, then it will really be a small stretch for Mozilla to combine FireFox and Thunderbird.
My guess is that there is a good chance that Thunderbird 3 will make its debut in Ubuntu 10.04 (LTS) Lucid Lynx.