When the Enterprise is pulled into the Borg Trans-Warp conduit, the effects shown while in the conduit are reused scenes from when the Enterprise was trying to escape from the energy vortex.
When Seven of Nine tells Janeway and Tuvok about the Multi-Kinetic Neutronic Mine, the visual diagram displays a model that has the exact same configuration as the renegade Borg vessel from Descent.
Stephen Hawking mentions being on the show, where he appeared portraying a hologram version of himself playing poker with Data, Albert Einstein & Sir Isaac Newton in the opening scene.