Currently I only offer point commissions because they're easier for me to do and usually when I charge real money, I do more complex commissions I base my costs on time used and the level of complexity and multiple characters. Maybe when I have more art I'll charge real money
I price in real money, because its not worth my time to be paid in something I can't use to feed me.
I generally weigh the options of its importance, ie, if its a small commission for someone for a present, not as much as something commercial. Then the complexity, how long will it take me, in honesty. I do usually underprice but not too terribly, I need commissions for practise, if anything.
I price in real currency (USD) but if people want to pay in points I just use the premium content system to get the equivalent amount of money. I price both on average time, and complexity. I never have set in stone prices either, I have rough estimates and then price commissions on a case by case basis. Prices also depend on if the piece is just for personal use or commercial use, and I charge a lot more for the commercial use ones.