AGP and PCI-E aren't compatible. In other words, no, AGP cards won't fit into PCI-E and vice versa.
Also (don't quote me), there might be physical size differences between x8 and x16 slots, just as there are physical differences between the x4 and x16 slots. There are x4 slots which are physically the same as X16 slots, and there are x4 slots which are physically different. I don't see why x8 slots cannot be the same.
However, just like how x4 cards can be put into x16 slots (even though its much smaller), x8 should fit into x16 slots. Doesn't work the other way around.
Although I mentioned that its possible for x8 slots which are smaller than x16, I didn't say that there are. They might be the same as x16 slots, but run at x8, in which case, x16 cards will still be able to be run on that slot, just not at x16 speeds (which I dare mention no cards are fully utilizing at the moment).