There is a recent trend to put small and increasingly powerful PCs on board UAVs, with an installation of GNU/Linux and specific software for robotics applications. For instance, Ubuntu and ROS, MOOS, etc.
Sounds great! Have you tried Raspbery Pi with Ubuntu + ROS? Or do you use your own custom program in linux? Ascending Technologies use a single board PC featuring an Atom processor and with Ubuntu + ROS installed by default, but the cost is much higher.
We haven't tried, see http://www.ros.org/wiki/ROSberryPi/Setting%20up%20ROS%20on%20RaspberryPi
If man hours are cheap, one may try a build of ROS. However, some GPIO programming and interfacing will be required too. A practical problem is that the peripherals may consume more power than the board itself.
I've searched around and found that there is an SD image with Raspbian + ROS (without Rviz) available here: http://jeremy-nicola.info/2012/10/05/new-ros-fuerte-sd-card-image/ . The author said that a tutorial on how he did it will come soon. I think I'm pretty much convinced that Raspberry Pi is a pretty good option! Thank you for the information.
I have used Gumstix Overo for Extended Kalman estimation of attitude angles. It's a promising platform. There are different versions, with high processing power (can go over 1GHz). It also supports different communication protocols, for peripherals. Also it there are some open-source libraries for image processing.