As for security, it's following closely the footsteps of Firefox, improving upon what is already in Thunderbird 1.5. Messages will be scanned for URLs, as well as common phishing tactics showing warnings as such. Nothing particularly out of the ordinary there.
The organization aspect is what interested me the most. Thunderbird 2.0 will bring the much-anticipated message tagging feature, which will let you sort mail into groups and prioritize them. The improved search features also integrate accordingly, letting you easily search by tags. You can also save your searches, which is useful if you tend to look for certain groups of messages multiple times. They also have added the very useful message notification, akin to what many apps such as Google Talk do. Some other popular Firefox features have been carried over, such as “Find as you type”. Ease of use is also improved upon, with better integration with services such as Gmail. Rather than having to get server settings and worry about specific configuration, you can simply supply the client with your username and have it done.
While no firm release date for 2.0 (early next month?), RC1 is expected by the end of this week. All these features aren't coming at the cost of bug fixing, thankfully. You can see a laundry list of bug fixes for the client at the Rumbling Edge log.