[asid61]

This looks pretty solid in terms of functions, and I like the use of transistors for the LEDs and the like. However, the resistor for the quadrature LEDs should go after the transistor, or you'll short your encoder outputs to GND.
As a side note, EAGLE does have an "LED" part in the default libraries, so you don't need to use a diode. Also, try using 2.2k resistors for your leds intsead of 100 ohm. 100s will probably cause too much current for the led, and 2.2k makes it plenty bright for indication purposes.

I love the limit switch LEDs. Optional pullup resistors are great. You might want to try one of those header bridge thingies to switch between 5v and 3.3v (possibly also for the pullup resistors). Solder bridges make it hard to change without a lot of hassle.

The one major problem I have with this board is that it's far to large. You can easily cut this down half the size. If you switch to soldering in headers instead of using solder pads, you'll save some space that way. At the very least, you can put all the solder pads on the "bottom" layer (facing up IRL) to let you shrink things down. I'm also not sure why you have so many holes in this thing; I would imagine you need 0 if it just plugs into the Talon The ziptie thing is a nice touch actually. Furthermore, switching to 0805 package stuff makes it sort of easy to hot-air solder and stays compact (I'm not sure what you are using now).

Use the "smash" tool to separate names and values of components on the board. That lets you put the names where you want them most visible, and you can delete that values; those don't need to be on the board.

Have you tried pricing this out on Digikey?