Leonard mentions that the original Michael Myers mask used in John Carpenter's Halloween (1978) was a Captain Kirk mask turned inside-out. This isn't entirely correct. It wasn't turned inside-out, it was painted white, the hair was dyed brown, and the eyebrows were removed.
Leonard and Penny's first kiss happened in The Middle Earth Paradigm (2007), indeed during their first Halloween together. Most of what she says occurred in that episode, except for her vomiting in a pumpkin, which must have happened off screen.
In this episode, Leonard is dressed as Inspector Gadget for Halloween. In the Inspector Gadget (1983) cartoon, the Inspector had a niece named Penny.
When Sheldon is upset at Howard's Halloween costume and in his office talking to Amy, he is wearing a green shirt with a circular design on it. This is a visual representation of the mathematical Fibonacci sequence where you find the next number by adding the previous two together (1, 1, 2, 3, 5, 8, 13...)
Sheldon's first costume is Dr. Emmett Brown (Christopher Lloyd) from Back to the Future (1985). Lloyd previously appeared on the show in The Property Division Collision (2016). When Amy visits Sheldon in his office, she is indeed dressed as Clara Clayton (Mary Steenburgen), Doc Brown's love interest in Back to the Future Part III (1990).