The painting in Widmore's office shows a balance weighing white rocks on one side and black rocks on another as equal, keeping up with the white and black myth.
While they are trying to restart the electromagnetic "Hydra" station, Seamus calls the rabbit they are using for their experiments "Angstrom." This is a double reference: 1) an angstrom is a unit of scientific measurement that expresses, among other things' sizes, the wavelengths of electromagnetic radiation; and 2) novelist John Updike wrote a popular series of books featuring a main character named Harold C. Angstrom, whose nickname was "Rabbit."
When Desmond visits the Widmore estate, Daniel is playing "Fantaisie-Impromptu in C-Sharp Minor", by Frédéric Chopin, the same piece he played as a young boy in The Variable (2009) and the same piece that David Shephard plays at his performance in Lighthouse (2010).
Also Eloise is wearing broaches that are reminiscent of the markings made on the world map at the Lamppost Station.
The drink Charles and Desmond share is MacCutcheon, the ostentatious whiskey seen many time through the series. In the flash-sideways timeline, Widmore tells Desmond he is "worth it", but in the original timeline, he is deemed not worthy.
The MRI Tech would not ask Desmond questions about metals, jewelry on him,or if he had metal in his head and bullets in his body while he was already in a gown on the table. These are pre-screening questions prior to getting accepted for an MRI. Plus he had a head CT so they would know if he had metal in his head or not.