I use a variety of input devices at work from a Thinkpad trakpoint, trackball, bluetooth mouse, Apple's Magic Mouse, and Apple's Magic Trackpad.
Depending on the operating system and computer I am using, my favorite mode of input changes.
For example, when I am programming on my Thinkpad T420, I prefer just to stick with the rd trackpoint. Even docked at a desktop, I stick with the red nub because I prefer not to move my hands around so much as I am typing.
When I am on a Linux tower workstation, I use Microsoft's ergonomically trackball. In general, I don't like using regular mouses if I can avoid it.
When I am on a Mac, I'll use the Magic Mouse if I am with an earlier build of OSX (10.5-10.6). But if I am on Lion, I use a trackpad.
As for my current favorite would have to be the any variation of Apple's trackpad - Macbook or Apple's Desktop Magic Trackpad.
In Lion, the multi-gestures is pretty incredible. I can't explain it. Two finger swipes is even more intuitive than using the forward/back page buttons on my Thinkpad. Four finger swipes across virtual workspace makes up for my mac's 13" 1280x800. In fact, Four finger workspace virtual space swaps allows me to be more productive on a 1280x800 screen vs my Thinkpad's 1600x900 screen. Despite the smaller resolution, I can swipe between applications effortlessly. All the gestures on Lion have pretty much awesome. No other company even comes close. I looked at some of the efforts by the Ubuntu team to bring these awesome gestures to the Linux world because I am looking to use my Magic trackpad on other devices beside a macintosh.
Here is a good video on multi-gestures in Lion on youtube:
Apple's Magic Trackpad is a great desktop device and my only wish is for a larger one.