Footage from Star Trek: First Contact (1996) is used for the flashes of memory that Picard experiences while on the Borg Cube. Several distinct sequences featuring the Borg on the Enterprise-E are shown in split second clips.
Soji has a box with the words "The Adventures of Flotter" and an image of Flotter, played by Wallace Langham, from Once Upon a Time (1998).
In Homer's Odyssey, nepenthe was a drug to quiet all pain and strife and bring forgetfulness of every ill.
The hug between Jean-Luc Picard and Hugh was not in the script. It was something that Patrick Stewart and Jonathan Del Arco wanted to do.
Rios and Raffi have a wager on finding Soji alive. The stake is two bars of latinum. This is an intergalactic currency used outside the Federation and particularly coveted by the Ferengi. It was mainly featured in Star Trek: Deep Space Nine (1993), usually as a macguffin in humorous stories.