In the opening, Annie and Britta argue about whether Troy and Abed's apartment is 303 or 304. This is a reference to the fact that this episode and episode 304 Competitive Ecology were aired out of order.
'Evil' Abed's suggestion on wearing goatees at the end of the episode may be a nod to 'Mirror' Spock from the Star Trek Episode 'Mirror Mirror'. In that episode, the audience meets a parallel 'Evil' Spock who sports a similar goatee.
At the end of the episode, when Abed is talking about "the darkest, most terrible timeline and creating the fake "Evil Goatees", there is writing on the chalkboard in the background, it reads; "Please return all books left in Study Room to the front desk. All special items were turned in at the Student Union BLDG. Have a great weekend.... My bad, see ya tomorrow." There is also an indication of the episode number "Tg 303" in the top right corner. This is seen as further proof this episode, and "Competitive Ecology" (S3: E3) were shown out of order.