(at around 35 mins) When Darcy picks up her TASER X26 from her bag (right before Jane backs into Thor outside the hospital), the sound of a pistol slide being maneuvered is heard. The TASER X26 does not have a slide or any moving part that can replicate that sound. Also, Darcy only picks it up and turns it around before putting it back in her bag, she doesn't move anything (safety, cartridges, battery pack).
(at around 1h) When Thor is led away after getting cuffed (after his attempt to retrieve the hammer), it is obvious that there is only a white, plastic loop keeping his hands in place. Despite the fact that we have heard the sound of cuffs. The loop is also not tight enough to serve as cuffs; it only serves as help for the actor.
(at around 43 mins) The hammer landed about 50 miles to the west of the town (according to the man in the diner). When Sif and Co. arrive, the SHIELD agent at the console says that it was about 50 miles to the north-west (at around 1h 17 mins), placing it 75-80 miles from the town. Yet, when the Destroyer arrived, which was at the same location as Sif and Co, it was clearly on the outskirts of town.
(at around 1h 21 mins) The coffee cup on the dashboard in the SHIELD agent's car is knocked over by the vibration of the Destroyer's arrival, in the next few shots of the same scene the coffee cup can clearly be seen inside the agent's car still standing up on the dashboard.
(at around 1h) Thor is soaked and covered with mud when he drops down in front of the hammer in the SHIELD enclosure. When he is led away by the guards, the shot is of a very clean man in a clean navy blue top.
(at around 1h 35 mins) Thor is holding his hammer in his right hand while he comes to the Bifröst and confronts Loki. When Loki sends him flying and he falls on his back and his hammer hits the floor, the hammer is in his left hand. It's back in his right hand after he gets up.
(at around 47 mins) When Jane, Erik and Darcy are on the roof of the garage after SHIELD has taken Jane's stuff, there is wind in their hair in the shot from one angle and no wind in the same scene shot from another angle.
(at around 1h 24 mins) When Destroyer fires at Thor during the attack on the town, Thor rolls towards this left in the air to avoid the explosive next to him on the ground. Thor is wearing what appear to be black glasses, possibly to protect the stuntman's eyes from the flash of the explosive next to him.
Thor has the ability to summon Mjölnir from distance (when it is in his possession - when he is worthy). He should have known that if he could not summon it from the town (or from any other closer location traveling towards the crater), he will not be able to take it from the crater also.
The goof items below may give away important plot points.
(at around 1h 40 mins) After the destruction of the Bifröst, Loki is dangling from his staff that is held by Thor. Loki is gripping the staff at least 3 feet from the bottom. As the discussion continues you can still see that his hand has not changed position but at the very last just before he makes the decision to fall he is only gripping it about 4 inches from the bottom.
(at around 1h 30 mins) When Loki is on his way to the Bifröst on horseback to destroy Jotunheim, he is wearing his helmet. As he is actually activating the Bifröst, his helmet is absent. The scene cuts to the Bifröst destroying Jotunheim for a few seconds before reverting back to the Bifröst interior where Loki is once again wearing his helmet, presumably just removing his staff from the activation.
(at around 1h 30 mins) After Frigga embraces Loki after he kills Laufey in Odin's chamber, she removes her arms from around him. When she turns around at Thor's appearance, her left arm is still on Loki's shoulder.
(at around 1h 30 mins) Jane is considerably shorter than Thor. Near the end, they are talking and she has to look up at him. When they kiss, she is suddenly at eye level. If you watch the horizon behind them though, you can clearly see that this is because the camera is tilted and Thor is bending down.