MikeH:
This is a great subject and one that probably gets more than a little controversial not just in play but in discussion on here.
I think the most significant of these kinds of examples are the ones that were sort of "in play" not out of play as you mentioned.
I don't know if it's apocryphal or not but they say those rocks in the middle of that par 5 at Nicklaus's Sherwood (whatever its name) fell off a truck and Jack sort of liked the look of them laying there so they remained. I guess Duval wishes they hadn't fallen off the truck in the first place.
Two of the more famous really quirky architectural features "in play" were probably those two massive in-line rolls on either side of the 12th green at GCGC and the famous "pimple" on the 18th green at PVGC.
They were certainly ultra-quirky and some on here think they never should've been removed and that they should be restored. I'd sure consider something like that but I would not consider it ONLY because the original architect built it. I'm interested in that but I'm also interested in finding out exactly why they were removed and I'm interested in finding out as near as can be just how they really did work in play.
I doubt there's a single person on here who's old enough to remember them "in play". But they certainly were radical, controversial, probably very interesting and even humorous---a number of things that are not bad things to have ever so occasionally!