NOT gate with an NPN (2N3904) transistor not working?
A 10 K ohm resistor, as a collector resistor, with a 0.7 Volt drop VCE, with   a 3.0 Volt source, will result in a 230 microamp flow, aka 0.23 milliamps. With a hfe gain of 100 as ideal, that's 2.3 milliamps at best VCE. But a 10 K ohm resistor as R2 would only allow a few micro amps through a led, not lighting it up. Try replacing both R and R2 with larger resistors and it will work. Try 470 to 1000 ohm.