Here's an example of 4 MAX7219's driving 256 LEDs.
If you think of each LED as being at the intersection of two wires, and you put a 2-pin header there instead, you can remote the LEDs and put them in whatever configuration you'd like. I think you can see from the attached how easy it would be to have an 8x16 header that you would add wires to remote-connect the LEDs. The MEX7219 controls the current so only 1 current limit resistor is needed.
MAX7219's are $1.25 from taydaelectronics, and seem like a great way to drive 64 LEDs. $5 for controlling the 256 LEDs pictured here. $12.50 for 10 chips, 640 LEDs.
It can do 15 level of brightness control also.
If you need RGB mixing control or fancier fading control, then other chips might work better, but you will need a lot more of them, or work out some multiplexing scheme; multiplexing would reduce the overall perceived brightness.
