That latter circuit may not work at lower voltages because you know have to add the voltage drop of the b-e junction(.7) to your led(~2.1-3.8v?), so the normal way as someone exampled give you. 7v more ability to lower the voltage
also 16Mhz is to fast too run reliably at 3v, maybe 8Mhz is a better way to go if you are going to be a lower power situation
it all wont matter if your not intending to lower the voltage in the project
and try a decent 5v supply instead of usb, I've had similiar problems with voltage drop from loads cauding problem