The whiskey William Bell is drinking when he's a cartoon is MacCutcheon, the same fictional whiskey Charles Widmore drank on Lost when he met with Desmond. J. J. Abrams was also the producer of Lost.
The glyphs for this episode spell out: FEARS
The running joke of Walter having difficulty remembering Astrid's name is used again. This time he calls her "Astro". Now, she's had enough, and responds by calling him "Wally".
The Observer strolls through the halls of the hospital after Bell/Olivia are wheeled in for treatment.
In the opening attempt to transfer Bell's consciousness to a brain-dead individual obtained from Harvard, Walter asks, "Are you ready?" Bell/Olivia responds, "Aye, Aye, Captain"--a common reply to Captain Kirk from Nimoy's tenure as Mr. Spock, aboard the Enterprise.