I'm trying to make an Arduino clone that has built in perf board area and is routed to fit a specific enclosure. It seems to be very hard to find a component arrangement that looks decent and is functional. Can anyone take a look at what I have so far and tell me where I'm going wrong? My earlier version had the ATmega rotated 90 degrees compared to this, but I just couldn't route the I/O pins.
My eagle board layout is: 
Thanks
Looks good to me.
Wouldn't you like to have some SOIC pads as well?
Thanks for your reply. I always meant to add SOIC pads and completely forgot so thanks for that. The perf area is already a lot smaller than I intended and I'll lose a little more that way.
To me, the layout looks very sloppy
Maybe you can improve on it if you break the extension headers, more like Arduino, into 2 banks, on both sides of the Atmega chip.
No need for reset button?
No automatic reset when upload sketches? (Either that or the decoupling capacitor is missing.)
The EAGLE autorouter is "not great."
It looks like the combination of routing grid, part positions, and design rules that you are using is not allowing traces to go between the pins of the AVR (or other 0.1inch-separated pins.) If you're having the PCB made professionally, there is no reason to prevent this.
you might want to route at least power and GND traces manually, using wider traces than most of the signals.
it looks to me like the LCD connector is in a bad spot/orientation, blocking the "obvious" routing between the AVR and the IO pins.