I've done a bunch of prototyping on both the Pi and the Arduino. For projects that I need to build more of, the Arduino is a better platform -- it's not copyrighted or trademarked or anything, so I can buy an AtMega chip and put it into a custom-designed Arduino-like board that does what I need. That's not true of the R-Pi. But then, the R-Pi is a MUCH more powerful platform. I mean, it runs Linux fer cryin' out loud.
I used an Arduino to set up a brew controller, when I should have used a Pi; turns out the Arduino isn't capable of anything like multi-threading operations, it takes a LONG time to get a reasonably accurate reading from a thermocouple, so updating a PID controlled SSR is too slow to get the ultimate accuracy that I need. So I'll have to re-implement that solution with a Pi. Meh.
My other fun project is using an Arduino to run an ultrasonic sensing system to tell me how much beer is left in my kegs. There are a lot of interesting engineering challenges, but it's a fun time.
Right now, I'm trying to figure out why I get really clean signals in the lab, and really noisy signals in the kegerator.