The Prado allows you to take pictures without flash of almost everything. If you use a flash, the guard will come and yell at you but they won't bother you for taking any other pictures. I imagine there may be restrictions on special exhibits that they do not own. That is the same with any museum.

The Reina Sofia has signs everywhere saying not to take pictures but last Sunday I went in and nobody told me to check my camera. I took plenty of pictures without flash until finally one guard told me no pictures. He was nice about it but they won't kick you out or arrest you. I'm sure I wasn't the only stupid tourist that did that!