These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Community S 3 E 08 Documentary Filmmaking Redux
Fridge Horror: Does the Dean simply own a copy of Jeff's underwear, or did he steal them from Jeff?
This may be a call back, since Dean Pelton was looking pretty closely at them during the billiards contest in "Physical Education."
And of course the previous episode showed that he's not above buying matching outfits.
Genius Bonus: While Abed diagnoses Annie as having Stockholm Syndrome, she is actually displaying a phenomenon psychologists would call "insufficient justification." It all starts when someone goes through a lot of effort/pain, and doesn't have a really good reason for why they did it, so they try to convince themselves otherwise. She's basically reducing her mental distress by convincing herself that the Dean is a genius, therefore justifying all the work she's done, since there wasn't any real reason for her suffering at all.