From EngBlaze comes a great article on turnings a rats nest of wires into a circuit board. The article is filled with good tips!
I've quoted four sections of the article below. Trust me, I know how easy it is to make these mistakes!
The Full Article
Double check RX and TX pinout
In standard electronics nomenclature, serial TX stands for “transmit” and RX stands for “receive”. Unfortunately, part manufacturers aren’t always so kind. On some devices, TX is an input and RX is an output, defying all logic (or using some twisted reasoning where you need to tie both “RX”s and “TX”s together). Even if they do use the normal notation, it’s easy to get things crossed up, so make sure you double check your prototype connections before you implement them in your PCB schematic.
Check the overall footprint of your board
Notice a theme with the checking yet? Welcome to the wonderful life of an engineer. As a real engineer, you’re responsible for real things, often expensive ones. As un-glamorous as it is, double checking just about everything ensures that you only have to make that expense once, not twice.
In this case, it’s important to check the footprint of your board to make sure that your components are placed and sized correctly, and won’t get in the way of each other. The best way to do this is to print out your silkscreen layer 1:1 on paper. If you have chips or components that you’ll be using on the board, place them on the paper to see if their footprints are correct.