The Biofoam. A dedicated Halo fan knows what Biofoam is, and the canister that sprays it fitting the exact description.
Going by the description, its the same stuff that Simon used on Zoe's injuries in the movie. The name is, however, a shout-out to Halo.
Mal and Jayne later take on call signs based on Voice Acting roles their actors later played in Halo 3: ODST.
Most obvious occurs in Mosaic, where Mal beats down several pirates with a sledgehammer, and River subsequently dubs him Captain Hammer. Along with a few quoted lyrics and lines from the musical, including Someone maternal! and I think this is what pain feels like....
There's a sort of Dark Reprise later on when Mal, suffering under the weight of The Chains of Commanding, pushes everyone else away and tells them "I'm fine," echoing a similar line from Doctor Horrible - in which neither of them are fine.
River also has a Dark Reprise when she echoes Mal's earlier "A man's gotta do what a man's gotta do" line...except this is right in the middle of an emotional breakdown. It reflects the dark nature of the source of those lines in a very subtle manner.
A very, very subtle one occurs in the epilogue of the Adrift arc. Wash comments that he hopes Mal won't bake him a "Big Damn Cake," to which Zoe replies that he's probably just kidding, which means that the cake is....
Various bits of information relating to the Academy are steeped in little references here and there.
Subject John 000-117, who incidentally also happens to have the callsign of Echo. Later followed by another test subject whose name is Sierra. River, incidentally, happens to be Alpha.
One of the doctors at the Academy is named Kondraki. Another is named Clef, and there's also a Doctor Brinks. Another of the test subjects at the Academy is named Wade, and there are also references to "telesthetic amplification" mixed in with the technobabble.
The codename for the entire Academy project is Cerberus.
River's sixth sense for electronics contradicts the theory of a scientist named Gallifrey.
In the "Silver" arc, Jayne comes across an artifact in a museum: an "electrosword" owned by an Earth That Was general named "Jingwei."
In the Third Interlude, River quotes Gandalf at Wash. Also, the chapter has an opening suspiciously similar to Blood Rites, with Mal and the crew being chased by angry bad guys hunting for a box of puppies.
In Chapter Six of "Charity," River mentions they could all be killed by a deorbiting toilet. That same chapter also has a captured mercenary who is thin, blond, handsome, rather talkative and forthcoming, speaks with a vaguely Spanish accent, and whose name is "Zev."
Inara's high-tech-looking bow is referred to as a "torque bow".
In the epilogue of Mosaic, when Mal asks River about what happened to her, River starts refering to herself in third person and says, "But she doesn't want to be there. She... I... doesn't want to go back," which is very similar to the dialogue from the "I Remember Me" mission in Mass Effect 1.
"Blanks," or people who are immune to psychics, are a possible reference to Warhammer 40,000, which originated the term.
In "Last Man," the flashback to Jayne's encounter with the Six Rifles takes place in a town with a climate that distinctly matches the Northwestern United States. The town is named Fallbright.
A possible one to Assassin's Creed in chapter 75. After spending time with Doctor Abu Mustafa Muhammad Ibn Haroun al-Rashid, aka Old Man Kickass, River mentions turning deadly leaps into glorious leaps of faith.
When River is punching her way through multiple SWAT teams unarmed, the gunship pilot pursuing her tells his dispatcher that he's starting to root for her.