I can speak from the angle of upgrading to the Clamshell series from the 5600.
I love the integrated keyboard. It is much, much easier to type on the Clamshell than it is on the 5600, and I use my Zaurus mainly for development and fun. The 5600 was a great device, but I felt that the large lack of support for it is its major drawback. I'd imagine that's how it is for the 6000, seeing as how it just recently came out. The C860 that I have has a huge support base, and that makes it so much easier when it comes to wanting something. The 5600 barely had anyone that had it, everyone had a 5500. I'd imagine with the 6000 it's practically the same, seeing as how it's brand new. I'm sure in time though it'll pick back up.
Personally, I say go for a clamshell series. It really does pay when you can fold down and protect the screen, and it is much easier to type with the wider keyboard. Applications are more than plentiful and it is very stable.