Here's a few of the little things I've noticed:
* When Geralt goes to sheath one of his swords, he hits the bottom of the sheath with his hand to nudge it up. I only just noticed tonight!
* When killing a monster or enemy. If they land in water the water surrounding that enemy will turn red with blood (very cool).
* The portrait of Ciri in the emperors study has a very unhappy face! She looks very sullen and annoyed.
* Ciri has scars on her belly that only come into view at certain angles when her clothing shifts.
* Some of the barbers are made to look like Salons, it made me laugh a little.
* The water in some spots (I think mostly Skellige) is an incredible green blue near the rocks on the coast.
* Vesemir's nose is slightly red - giving him the look of an old drinker lol.
* Keira Metz walks barefoot.
* The damage from Kaer Morhen that was left by the Frightner is still there
* The armor the baron wears is covered in tiny dings and scratches and when the light hits his armor it really shows.
* Triss has the tiniest freckles on her nose and a small beauty mark on the left side of her lower mouth. Her forehead also wrinkles when she talks.
* Djikstra's wears a fancy doublet like most of the wealthier NPCs in game, however, the buttons in his doublet sleeves are all undone (because the sleeves probably wouldn't fit otherwise).
* The fabrics on characters and the skin goes shiny when the rain comes on (nice touch).
* Sometimes specific graves can be found in areas that might relate to quests or People NPCs might have mentioned (even if you didn't necessarily have to go to the site as part of any quest, their being there is a nice detail).
* The way the trees sway in response to the weather system
* The background music seems to be different in Skellige than it is in Velen, it has a more Celtic sounding lull about it.
* Roach's appearance changes depending what accessories Geralt puts on her (there is more than one style of Saddlebag and saddle for example (also only just noticed tonight).
* the other notices on the boards that aren't contracts are sometimes hilarious
* the patchy and damaged look of some of Geralt's armor showing tears and dings.
* If Geralt saves the Fake Witcher from the towns people during a contract/side quest and tells him he has to make amends by working for the townspeople, later you can find the fake Witcher working in a field digging, lol.
* finding money in random old tree trunks in the middle of nowhere with no relevance to any quests.