LED on ATMega328 dimmer than expected
Essential for the brightness of the LED is the current through it. Different types of LEDs have different nominal currents. Typical is 20 mA or 2 mA for low current types. The ATmega can typically drive 40 mA per output pin. Assuming your supply (the programmer in your case) can give you enough current, you have to correctly set up the port pin in your source code by setting the appropriate port direction register and the port itself and you have to calculate the value of the series resistor.

This resistance depends on the output voltage of your microcontroller, the needed current through your LED and the voltage over your LED which basically depends on its color. For example a standard red LED has a little less than 2V and 20mA. With 5V from the controller you have 3V over your resistor, so to get 20mA through resistor and LED you need 150 Ohm. If you don't have a datasheet for your LED you find values for different colors on the web or even a series resistance calculator.