I only season I currently own is season 1 on blu-ray, so here som observations I've made over the years on many formats.
Man Trap.....At the end when Kirk says, "I'm sorry Bones." a rather large moth flies behind his head.
In Charlie...When Charlie hurls back Kirk/Spock---Nomoy's knee breaks the (dry)wall of Rand's cabin
In Galileo....When Gatano gets the phasers from the compartment the actor completely misses the button.
In Galileo..when Boma sticks his head in the shuttle to say something you can see a stagehand (or the actor himself) shut the lower panel manually
In Balence....especially noticable in blu-ray....when kirks gives his speech to the crew his Toupee at his 'widow's peak' has begun to peel away from his skin. it's the most noticable I've ever seen his toupee peeling.
In City....the coffee Edith & then Spock pour is giving off NO steam.
In Where No.....the shadow of a boom mike is very visible in Blu-ray on the green wall behind Mitchell/Dehner in sickbay
In Enemy....the insert shot of 'evil' kirk's phaser is the larger (type 2?) and he clearly has the smaller one before and after. (Although he stole the larger style one from Fisher in the first place)
In Charlie...when Kirk talks to charlie in the corridor before charlie tags along to the bridge, Kirk's shirt has shrunk so much that the entire zipper seam is stretched to the limit.
In Charlie....when Charlie is on the bio-bed doing the leg pump, the insert shots show the actor's reflection in the glossy readout area.
In Man trap....when Sulu touches the 'deceased' Barnhardt his eye noticably flutters. (Barnhardt's eye that is

)
In Man Trap....I read that the actor playing Prof Crater separeated his arm the day before the shoot & was in great pain. You can see he favors it through-out the episode. It sags low and he keeps his right hand in his pocket often--even when running after 'Nancy'. What a trooper.
In Enemy.....when Kirk applies the make-up to his scratches you can see that the mirror, that they have in all their cabins, have beveled edges. To prevent the upper beveled edge from picking up boom mikes, lights or rafters they have placed black electrical tape over ONLY the upper bevel. I only saw this on Blu recently.
In Where.....when they show Dehner/Mitchell's bios you can it looks like they used 'white-out' to alter the statistics.
In Enemy.....I find it funny when Sulu heats the big rock, instead of all 4 huddling around it they form a front row/back row formation.

What rank do you have to be to sit right next to the hot rock?
In Man Trap......... as Nancy first approaches she is singing but her mouth is not moving. Or did she hypnotize me into thinking she was singing?
Man Trap.....when Crater blasts the middle pillar (of 3), holding up the arch---Kirk takes cover under the same arch

Did he teach tatics at the academy?
Man Trap...as kirk crawls along the ground his communicator keeps popping open, but makes no sound.
Naked Time......Sulu sword is bent on the end---his foil that is.
In Archons.....a huge rock hits Lindstrom on the head----no effect!
In Archons....Sid Haig (lawgiver #1)was just as ugly in 1966 as he is in 2009.
In Archons....the door the crew runs into is diiferent from exterior/interior..Same with the window Kirk looks out upstairs.
In Archons....why doesn't Sulu at least hold his ground & bat away the 'hollow tube' as the lawgiver approaches? He only needs seconds for the beam to take him.
In Shore....why does the black knight's face look so fake? I know it wasn't important that his face look normal under the visor, but was the 'caretaker' saving money on the 'good fake skin' ?
In Shore....they of course switch back and forth between US & Jap. aircraft.
In Shore....you can see the chain around the tiger's neck as they run past.
I have hundreds more, but this is a gigantic post as it is---so i'll post more later.
BEWARE POPO BAWA !!!