That's not a place for a cap. That\s a place for a jumper wire or jumper pin for optionally powering the whole device from the Gameboy, through the link cable, if you have no other power source like USB.

But, like I mentioned, I would first solder all the pins of the pin header, and also to check if the microcontroller chip is oriented correctly, no joke.

I was told that jumper is necessary to power the board via the 5v pin on the cable. Perhaps I misunderstood. I'm still working on figuring this stuff out!

My mistake, for some reason I didn't think there was resistors for the LEDs, but that's clearly not the case...

you know im noticing you put a jumper wire between what looks to be a spot for a .1uf cap... it looks unnecessary.

Wow, didn't notice that. I think we got the winner here.

You are correct. I should've mentioned that exception!

The LEDs should give you no trouble. Because of the resistor, the current is limited, and the circuit will work fine both if any LED is unfitted, or if it's shorted. If the LED worked when you tested it but stoped working when you fitted it (assuming everything else is ok) it's more likely that you inserted it backwards than that it's broken. Inserting it backwards can NOT damage the chip, however. Never insert diodes used as rectifiers the wrong way around, however.

I'm noticing a lack of solder. If the board is anywhere near decent quality, the holes will be plated through with copper, so that if you solder on one side, there should still be a connection through the hole. I'm however noticing that the pin headers are not soldered (right?) That means that there's no guarantee that all the pins will mate. You probably should solder all these in place. (I'm pretty sure you didn't solder them on the bottom as there's plastic in the way. )

Another thing you might want to check is that the microcontroller chip is inserted the right way around. It sounds crazy, but there are images, official product images even, all over the interwebz, where the chip is inserted the wrong way around. (Knuckleheads!) The chip should be inserted so that the notch is pointing "down" i.e. NOT toward the side where the USB and power connections are.

If any of them are in backwards, it may cause it to not function at all. Edit: Disregard; present resistors will prevent the VCC-GND short.

As for the solder: With the through-hole plating, you should visibly see the solder on the other side. I don't see that in this case (at the zener diode, for example). This probably isn't causing any problems right off the bat, but may cause poor connections after time.

They're all recycled LED's. I thought I could get away with it, because I had them working on the breadboard. I did end up swapping one out, so perhaps it is an issue with the LED's.

I'll try adding more solder as well; I've got plenty on the underside of the board, but it can't hurt to be safe.

I appreciate the tips!

I'm assuming as there is what seems to be four or five different types of LEDs on the board, you are using recycled ones? Have you double checked the polarity? There seems to be insufficient solder on a lot of the components so I'd start there.

Could it be the problem of the link cable? Are all the pinouts connected correctly? It took me a while to get the right pinouts when using non official cables.

Alright, just tried a second atmega chip and no luck

Anybody have any other ideas?

The atmega. But it'd be an easy fix for you. You just reload the code. I couldn't do it because I didn't have a way to.

Do you mean the atmega chip on the arduino or the 8-pin opto-isolator on the shield?

When I did my arduinoboy the chip had apparently gotten too hot and caused similar problems. New chip and, poof, magic. I dunno if you made the same mistake as me, it's just the only thing from my experience.