I've got one each of the 50 mm f/1.8 AIS, AF-D, and E-series. In general picture taking, you can't tell which is which from the prints. Maybe if you blew them up to gigantic size and examined the prints very closely with a magnifier you might, but let's be realistic. In practice, other variables will easily cancel out any slight differences among them.
The 50 mm E-series lens is perfectly fine. I have no problems with the narrow focus ring. I'm told that the optical formula is the same as the AIS version of the lens and that the differences lie in the the manufacture of the barrel and the coating. It appears to be a bit less resistant to flare that the other two version I have, no doubt due to the fact that the front element is not deeply recessed. This is easily fixed by attaching a cheap rubber lens hood to the lens.
The AIS version of the lens is my favorite of the bunch, and I tend to use it the most on my manual focus bodies. It delivers the goods every time. 'Nuff said.
The AF-D version's optical quality is just as good as the AIS version, but I am not at all thrilled with the ergonomics of the thing when used as a manual focus lens. The lack of dampening on the focus ring is annoying and there is less travel from lock to lock. It takes relatively little movement of the ring to affect a big change in focus. It works really well in AF mode on my F100 and N90, and makes for fast street shooting on those cameras when they are set to one of the available AE modes. It also works great with TTL flash on the cameras that support it. You will be able to exploit none of these feature with the FM, so I'd skip it unless you plan to add a Nikon body that will be able to use them in future.