Creating negative Voltage with Arduino Mega 2560

dochawk:
but how much current can it supply

That depends on quite a few variables the ripple you are willing to accept.
Note that at any significant current, you "lose" 2x diode forward voltage (2x ~0.7V for standard Si-Diodes), so Schottky diodes might be worth it (2x 0.3-0.4V)

Some example values (Didn't test in reallife, this is simulated, assuming 100 Ohm output impedance of the arduino digital pins)

50kHz, 1uF, 15uF:
-1.0V: 7.0mA @ 0.2% ripple
-2.5V: 3.4mA @ 0.06% ripple
-3.3V: 1.6mA @ 0.02% ripple

10kHz, 1uF, 15uF:
-1.0V: 7.0mA @ 1.2% ripple
-2.5V: 3.4mA @ 0.26% ripple
-3.3V: 1.6mA @ 0.1% ripple

10kHz, 1uF, 75uF:
-1.0V: 7.0mA @ 0.25% ripple
-2.5V: 3.4mA @ 0.05% ripple
-3.3V: 1.6mA @ 0.02% ripple

As you can see, ripple is ~1/f and also ~1/C

I found that increasing the 1uF doesn't do much, but drastically reducing it will decrease the performance quite a lot.

Concerning the duty cycle: 50% is the "best" in terms of highest efficiency and output, but reducing the duty cycle is a possible way to closed-loop-control the output voltage.

It's far from linear though and low duty cycles will cause high current peaks on the arduino digital pins, so on your own risk.