I literally just learned yesterday about the "Search for similar Items" feature in Diablo III (right-click items to compare to similar ones at the GAH/RMAH). I literally searched similar items manually from the moment I started using the GAH (about two weeks after the game's release or so) until yesterday, filling up filters one by one and hitting "Search"... every. single. time....
That's the most recent one, but there's a good number of such "discoveries" I've made from older games even though I played most of those for months if not years. I have to say however that most of those cases are console games which I used to be renting many years ago. Because to be honest when I owned games myself there was very little that escaped my attention over time (but it did happen anyway).
One such "discovery" was way... way back (man I'm feeling old) when I bought the PS1 version of Command & Conquer (Gold). I had never played the PC version prior, and anyway... English not being my native language back then the manual (in English) wasn't helping me to learn about the game so. Yeah anyway, I learned pretty much everything over time, but there was one exception. I later found out (later... I.E. so much later that RA2 had been released and found out about it in RA2, but it worked in C&C1 or RA1 as well) that I could force-fire my units... not only that I could STOP an order I had just given my units (and also stop the force-firing).
Another one was in Turok: Dinosaur Hunter. I've played that game to death from start to finish a good dozen times back in the N64 days. Then years passed (try something like a decade or so). Then back in around 2006 or 2007 I bought the PC version from eBay. I played again for nostalgia's sake (and was still fun anyway). At some point I saw some grenade launcher rotating on itself, up in the air near some pillars. I believe it was in the second level. I recalled at that point that during all those years I had never figured out how to get there.
Anyway, long story short... I played again (that level), walked around and eventually "discovered" some relatively hidden way to get there but it wasn't that difficult (and I did try all those years ago). It involved walking onto a barely-visible platform of energy or something like that, and that energy was visible (barely) only around your feet when you'd point the camera down, so you had to look down while pressing forward to see if the energy started to fade out to the left or right, so you wouldn't fall down.
But these examples are nothing compared to the list of most likely hundred such cases I'd have to share (especially in action-adventure games or games with lots of exploration and little spots and secrets to discover).