For jeans, I would probably put thighs up there on par with waist. There's definitely a camp of people that size to thighs as the waist will stretch but the thighs less so. If you state in the description what type of rise they have you can typically get away without posting rise measurements. The other big one for me is leg opening. I don't really care at all about the knee.
For shirts, assuming short sleeve, chest and length are the two I pay attention to (in that order). For long sleeve shirts, as a tall guy I always look for the sleeve measurement as well. If it's not available I usually don't buy it unless the return policy is decent.
There's also a lot to be said for posting the model's measurements and the size they are wearing. I find that more useful than measurements a lot of the time.
Edit: And I realize I didn't answer your question. I would say laid flat (e.g. 17") is by far the most popular way of presenting the measurements.