Amber's wearing of a McGill University sweatshirt (Dr. Wilson's Canadian undergraduate university) slyly verifies Kutner's observation that "she has legs that go all the way up to Canada".
Hasidic Jews would not say "Shabbat" but the Ashkenazi pronunciation of "Shabbas." They would not pronounce the Sephardic pronunciation of "Shabbat Shalom" but instead say "Good Shabbas."
House reads the "Autobiography of Ashley Bowen" while waiting for Amber to arrive at her home. This was a "get well soon" message to Ashley Bowen who worked in the art department on several episodes but was in the hospital during filming.
House tells Amber he still calls her "Cutthroat Bitch" because "quod erat demonstrandum", a Latin phrase meaning "that which was to be demonstrated". It is often put at the end of mathematical proofs or philosophical arguments to indicate that the argument is complete.
When Wilson and House are speaking at the restaurant, you can see the Royal Diner through the window over House's shoulder. The Royal Diner was a central location in "Bones".