Above the Influence: Memorably in Leonard and Penny's first kiss, she was drunk and upset that she even invited Kurt to the party. Leonard knew the real reasons but couldn't take advantage of the situation.
Penny is not nearly as flighty and/or ditzy in later episodes as she was in the pilot.
In the pilot, Leonard describes Sheldon as a pro in masturbating, something the asexual Sheldon as we know him nowadays is far from. (This is a carryover from the unaired pilot, wherein Sheldon has even had sex with a female colleague).
Also on Sheldon, he was at first much wiser to relationships and social norms (though still awkward), traits that have been phased out in favor of EXTREME social ineptitude.
Foreshadowing: Leonard obviously still had a big crush on Penny, but backed off on longing for her while she was dating a guy named Mike. When she kissed him on his birthday those feelings flared up again and lead directly into the season finale.
"The Reason You Suck" Speech: Penny tells Leonard he ought to grow up and stop playing with science fiction toys and action figures. After Leonard takes her words to heart and starts to sell his things, Sheldon later counters with Penny's own collections of Beanie Babies and Hello Kitty items.
Recruited From The Gutter: In the original pilot Sheldon & Leonard take in a recently homeless woman and decide to reform her. She goes along with it mostly because she has nothing better going on in her life.