USB ports are theoretically rated to supply 5v at 500mA, which is enough current to run up to 25 normal LEDs at 20mA each. So USB power should be sufficient for a handful of LEDs. For example, JPACs run on 5v USB and look how many LEDs they support (5 or more), in addition to their video amp and keyboard interface functions.
Using 12v for LEDs is fine, but the wiring is a little trickier. Instead of wiring them all as single LEDs in parallel, you should wire them into series-wired arrays of three or four or five LEDs, with each LED-array wired in parallel. each array will need just one limiting resistor.
Look below for a great LED matrix calculator. this tool will tell you how to design your LED matrix and what limiting resistor to use depending upon your type of LEDs, current source and other specs. It will even draw a circuit diagram for you:
http://led.linear1.org/led.wizFor example, I could make an LED matrix using four red LEDs rated at 2.5v/20mA, wired in series behind a single 27ohm 1/2W resistor and run off the 12v rail. Total power draw would be under 100mA, well within safe range. You could then run four of these arrays in parallel from the same 12v rail, for a total of 16 LEDs with a 'safe' power draw of 400mA.