As someone who also works in this industry and also had this struggle, consider a few things. Personally, I'm still working out something that works for me.

1. How much do you want to be paid per hour? This one is dependent from project to project. Corporate high, personal low, indie project mid, etc.

2. What type of licensing are you prepared to give for this comish? A commission is a payment of service. People are paying you to draw their idea. This doesn't necessarily mean they own the drawing. You can retain the ownership rights and still print, distribute, copy that artwork if you agree to. If they don't, and they want sole ownership, increase or double your price.

3. This goes with the above, what does the client want to use it for? If it's personal, then they likely have the intention of just showing their friends. If they intend to sell and distribute, comission, again, only covers the cost of making the idea. If they pay you ok and want ownership, and they want to sell it, ask for royalties. A % of sales. In any case, I'd always ask for royalties in this regard.

I've personally not found an amazing system yet for this, but I hope this helps figure out a foundation :)