The Man from Another Place can easily be seen as a malevolent figure here. He may just be opposing BOB because BOB is hogging all the Garmonbozia from the other Black Lodge denizens, rather than for any noble reason. Similarly he might be MIKE's evil side judging by his comments that he is The Arm. And even if these interpretations are true he might still just be a case of Blue and Orange Morality acting in a way that seems evil but is ultimately alien in his motives.
MIKE can be seen as having faked atonement especially with his last scene where he and the Man from Another Place demand their share of the Garmonbozia. Instead of wanting to stop BOB for any good reason, he's simply after the Garmonbozia for himself. Or that was him denouncing BOB as MIKE had foiled his attempt at possessing Laura. Or it could just be a necessity for him to live, Heel–Face Turn or no. Or the presence of a man who may be the Arm he cut off which represented his evil was affecting him negatively.
The film also puts into question Leland Palmer's image as a good father. How much of his behavior is because of BOB's possession? Is BOB really controlling him, or is he just influencing him? Did Leland have a dark side that BOB fed on to make him do bad things or did BOB just create that dark side?
Les Yay: The hints of some sort of romantic attachment between Laura and Donna are more explicit in the movie than the show. The fact that Laura was only seen alive in one shaky home-video-style scene in the show kept things pretty ambiguous, but the film shows a Romantic Two-Girl Friendship that might have gone somewhere else if Laura wasn't so afraid that her sexuality in general would corrupt Donna.
Narm: Numerous examples, but none more narmy than Laura and James' exchange about being 'gone, long gone, like a turkey in the corn' - not helped by the fact that Laura's 'Gobble, gobble' anticipates another notorious narmfest, Gigli.
One-Scene Wonder: Loads of these. David Bowie shows up for all of a minute as Agent Jeffries (whose role in the shooting script was slightly larger), Harry Dean Stanton as a bizarre trailer park landlord, etc.
Tear Jerker: Dear God, the ending scene in the Red Lodge after Laura's death. We see Laura's spirit, despondent, until she sees that her angel has returned to her, and begins to smile and cry. Sheryl Lee's acting in that scene is something that has to be seen.