I've tended to shy away from simply throwing arduinos at my projects, especially if I don't intend to disassemble them once they're complete. Arduino's a great prototyping platform but I find custom designing a PCB gives me much more flexibility in layout, size and most importantly microcontroller selection.
My experience with ARM microcontrollers from STM and Freescale have strongly dragged me in their direction, however AVR remains the most hobbyist friendly solution. The scope of my project doesn't require too much out of my microcontroller, so I settled on the Atmega16u2 which is very similar to the 8u2 which modern arduinos use to provide a USB-serial bridge. The extra 8k of program memory eliminates the need for an additional microcontroller like the atmega328, significantly reducing the cost of the board at volume.