Some LEDs are rated at 10mA, some at 20mA. The D155, for example, is daylight readable at 2mA, and at 20mA will burn a hole in your eye (yes, I've looked at it).
The controllers are rated for a max mA per pin, but also a max mA per power supply/ground pin (total power sourced or sunk by the part). Do not exceed either of these.
I don't like tying controller pins straight to an outside connector. What happens if someone plugs a RS232 cable into this connector? Also, at what length will your two boards be separated? You may pickup some noise or experience a voltage drop that won't let the micro detect a "1" coming in. I would suggest at least a minimum of 100 ohms in series, and maybe a .1uF cap between the resistor an uC pin. Optoisolators work very well in eliminating board to board noise, and can switch 12V to 5V to eliminate v drop on your line. Unless, of course, you want the line to be bidirectional. These are just things to be considered, the most important of course is dependent on the distance your two boards will be separated by.
IC decoupling is very important, as mentioned by Mr. T, and in addition, put a couple of 10uF caps around the 5V rail, or close to the uC. You may not see any problems while you're developing your board, but proper decoupling can save lots of head stratching over random problems occuring in the field once the board is in use.
If you're doing ADC conversions, separate your VCC and AVCC with an inductor and capacitor filter.