The Man in the Yellow Suit - S1-E9
Trivia: The back pack that Iris gives to Barry has two references - the bag has the colors of the Flash in the comics, red and yellow, and inside there is a comic book of the space ghost, another super hero character.
Things You Can't Outrun - S1-E3
Trivia: As Barry is going up the stairs in the police station he says he doesn't want a museum dedicated to him. In the comics Flash has his own museum.
Tricksters - S1-E17
Trivia: When Jesse learns a new Trickster is copycatting him, he tells Barry and Joe that when he terrorized Central City, days without casualties were as rare as the Chicago Cubs winning the pennant. A few months after the episode aired, the Cubs made the playoffs, but lost the pennant in a four-game sweep; they won the pennant the following year and went on to win the World Series for the first time since 1908.