Hodgins, prior to diving into the fish tank, claims he looks like Richard Dreyfuss and then quotes him from Jaws (1975), "we're going to need a bigger boat." In fact it was Roy Scheider who said, "You're gonna need a bigger boat."
Dr. Brennan tells Booth that Andrew is taller than him, which is true, by 1 inch.
Dimitri Vladov, the Russian mobster, has the nickname of Vlad The Impaler. This nickname was originally attributed to a Romanian nobleman, who had allegedly killed thousands of people during his reign. He was also the historical inspiration for the fictional Dracula.
The fish that were brought back to the Jeffersonian were Angel fish. David Boreanaz had his breakthrough casting as "Angel" on "Buffy the Vampire Slayer" and was also the titular "Angel"
The aquarium is the Aquarium of the Pacific in Long Beach California.