Characters from other fanime series can be found in the backgrounds multiple times during 2.0, including Amy from Future Agents, paying homage to the creator Pilot Obvious.
If one also looks carefully, characters from the animator's favorite anime, cartoons, etc. can be found as well: Rick Sanchez, Lucy from Elfen Lied, Terezi Pyrope, Dave and Dirk Strider, John Egbert, Rose Lalonde, Asuka Langley, Rei Ayanami, and Konata Izumi.
In part five with the scene of the classroom, you can see under the "vocabulary" section of the left corner of the board, that the words underneath are "Critical", "Pictures", "XAINAX", "Temar", "Film", and "Industries". On the other side of the board you can read "Study, you lazy shits!".
The song "Perfect Day" used in part five during Dom's turmoil is a tribute to the 1996 film Trainspotting.
Hoffman being a canon character is debatable. Canonically in 2.0, he is an android modeled after the Gears of War canon character with the same name, who does not make an appearance with the film. He shares very little with Colonel Hoffman's actual backstory, including previously dating Bernie and Margaret. Technically Victor is an original character in 2.0, but is more specifically described as a modified canon character.