SparkFun created an ATmega32U4 board,
Pro Micro under CC-SA 4.0. The ubiquitous cheap clones use the Arduino Leonardo bootloader. I like the ATmega32U4 because of its simplicity and hardware USB 1.1 (12 Mbits/s, easily reaches a megabyte a second using e.g. USB serial endpoint). The HID support in particular is very nice: makes it very easy to create human interface devices like keyboards, joysticks, and gamepads. (I've also used one to simulate an USB-connected vinyl cutter I did not have access to, but had an USB data dump for, for developing/bug-fixing a driver for.)
With the Leonardo bootloader, in Linux, the best way to get them reliably programmed is to detach, wait a couple of seconds, then reinsert, wait a second, and click program in the Arduino environment; the timing is sometimes a bit tricky to get right. (Getting the Leonardo bootloader to properly trigger a firmware upload is the issue.)
You can obviously create your own bootloader, too, but I've not bothered yet. There is even an instructable, IIRC, on how to upload a new bootloader to a Pro Micro clone. If you want to play with making your own board variant, you could start with the Pro Micro at
EasyEda (an online circuit design tool).
As to Teensies, head over to
PJRC.com or the
forum there. Paul Stoffregen is the developer of Teensies. To create your own Teensy variant, you can create your own board based on the schematic (the board files aren't publicly available, I think), and buy a preprogrammed bootloader chip from PJRC.com. This is what others have done. PJRC.com funds the development by keeping the bootloader (including processor initialization part) proprietary. Note that Paul Stoffregen not only develops the Teensies and maintains Teensyduino, he also supports the Arduino environment, both via
fixing bugs and developing various
libraries (at
GitHub).
(I personally could be described as a rabid open source and linux advocate, but for cases like this, I definitely understand why keeping some parts proprietary is necessary for a very small company to fund the development.)