"I am not to the point of creating my own printed circuit boards yet (plus they're cost-prohibitive), "Not true - $10 for 10 boards 50xmm x 50 mm. $25 for 10 boards up to 100mm x 100mm. Very inexpensive.C1/C2 are needed for oscillator stability. Crystal is not mounted in a good place - put it much closer to the pins.C3, C4, C5, you want them close to the Vcc/Avcc/Aref pins and gnd.I don't include the diode in my personal designs, but I am careful about applying voltage.On my bobuino, I did include it - between the power jack and the regulator, just like on a duemilanove.For the 5V, put a couple of pins in and install a jumper for the source you are using - USB/FTDI or external.Do not run the FTDI 5V thru the input of the regulator - that will just cause it to be lowered.
Also, ground trace should not daisy chain from one component to the next, especially if one of the components on there is a crystal. Noise from internal switching on the microcontroller will get introduced to your ground all over that trace and will raise the 'potential', basically you won't have a true ground to reference anymore. Also, it's one long electromagnetic antenna, picking up radio frequencies. This could potentially effect your timing. If you were to redesign, I would recommend either learning about polygon ground pours or, at the very least, draw one huge fat ground trace up the middle of your board and have all components that need to reference off it connect straight to that, not each other.