Some recent moments for me: (Playing in a dark room helps.)
-Clearing out the spawns around daedric ruins at night combined with the monsters from Creatures and Morrowind Advanced plus the added sounds from Piratelord's Expanded Sounds. With the semi-maze created by the ruined walls in these areas, I always am at least little freaked out when I clear the area of baddies, since they can be very tough and the place is always crawling with them. This last time I thought I was right behind a silver saint when it went behind a wall and managed to come around behind me. When I turned around it was already right in my face. Had to change my greaves afterwards. Oh, and those daedric bats still catch me by surprise sometimes.
-Focused on picking the lock on a chest in a tomb and a disembodied voice yells "N'Wah!" at me right behind my right shoulder. Jumped out of my freaking chair and cried like a child. Thank you Haunted Tombs and surround speakers for another change of greaves. I've been playing with this mod for a while and it still catches me off guard at just the right moments.
-Final battle in Siege at Firemoth. Get's my adrenaline pumping every time. (Okay, so I've only done it twice so far, but still.)