Another Dimension: Hinted at twice in the second issue. The Doctor, who claims to know every star and planet out there, identifies Worf as a Klingon, but then informs Amy and Rory that until seeing him he'd never heard of a Klingon before. Later, when Picard receives the Distress Call from Delta IV, the Doctor reminds us of his familiarity with the whole of the universe and then states he's never heard of Delta IV. Guinan confirms the multi-dimensional nature of the conflict in Issue 5, explaining that part of what makes the Cybermen so dangerous is their awareness of and existence in multiple dimensions, and how assimilating the Borg and their resources would make them powerful enough to expand across and take over all of reality.
Art Shift: When the story flashes back to the Fourth Doctor meeting Captain Kirk, the artwork shifts away from J.K. Woodward's painted/photorealistic artwork (for the TNG scenes), to the Sharp Brothers' poppy Sixties look (for the TOS scenes).
The Assimilator: Both the Borg and the Cybermen, as per usual. Now working in tandem.
Bad Future: The Doctor uses the TARDIS to show Picard one in which the Cybermen succeed in assimilating the entire universe, in order to fully drive home the severity of the situation and persuade him to accept the Borg's help in stopping them.
Continuity Cavalcade: The trip forward in time the Doctor shows Picard in the Bad Future shows Vulcan, the Klingon capital (including Cybermen with Bat'leths), converted Judoon and Raxacoricofallapatorians.
The TARDIS and the Enterprise-D, natch. Issue 2 even has the Doctor complimenting the design of the Enterprise's bridge.
The Doctor: Lines. I like the lines.
Though the Doctor does note in issue 7 that while the Enterprise is a fine ship, he'd rather have his TARDIS under his feet in a crisis.
Distress Call: The Enterprise receives one while Picard is talking with The Doctor, regarding the attack on Delta IV. Garbled and incomplete, they don't learn who is responsible until they arrive.
Enemy Civil War: As of issue 4, the Borg and the Cybermen are now warring amongst each other, with the Federation seriously considering the option of simply sitting back and allowing their most hated enemy to be wiped out, in spite of the Doctor's warning that the Cybermen are emphatically not their friends.
Enemy Mine: In the face of total Cybermen domination, the Doctor makes it clear that the only way to survive is for he and the Enterprise crew to temporarily ally themselves with the Borg — a decision that Picard is obviously not happy with, given the torture he previously endured at the Borg's hands.
The Farmer and the Viper: More of a case of the Viper and the Viper, seeing as both the Borg and the Cybermen team up, knowing fully well that the other would try to assert dominance over the alliance at one point. The Cybermen were just better at it.
Gibbering Genius: The Doctor, to the point that Worf asks him to please stop talking.
Hive Mind: The Borg and the Cybermen, per usual. How combined those hives are has yet to be seen, though so far we've seen a Cyber Controller outfitted with Borg technology. Not very, as it turns out. Not only do the Cybermen turn on the Borg and almost destroy them but that was their intenion all along.
Ripple-Effect-Proof Memory: The Doctor demonstrates this ability in the second issue, but with a variation: he states he actually feels his memories changing, and says he didn't know what a Klingon was until he laid eyes on Lt. Worf. Later on, he notes that if his memories are changing, then they're in even worse trouble than he initially thought. Because of all this, Picard takes him to meet another time-sensitive alien with Ripple-Effect-Proof Memory: Guinan. See also Sequel Hook.
Save the Villain: In order to defeat the Cybermen, the Borg collective must be restored.
Shout-Out: Bordering on Ascended Fanon: the Fourth Doctor meeting Captain Kirk and the crew of the Enterprise is similar in many ways to a popular crossover fanfiction, The Doctor and the Enterprise, wherein the same scenario occurs.
Teleporters and Transporters: The Doctor is amazed at the teleporters. (Probably unlike the Transmats, they can teleport more than three people at the same time.)
Wacky Wayside Tribe: Issue 1 starts out with the Borg/Cybermen invasion of Delta IV, followed by the Doctor, Amy, and Rory capturing a fugitive alien in ancient Egypt before landing on the Enterprise's holodeck during a Dixon Hill program.
What Have I Become?: Inverted. Data explains at the beginning of issue two to Geordi that this is the reason he doesn't upgrade his hardware, as he would wonder, over time, how much of him was left in a reinvented self.
What the Hell, Hero?: Riker has this reaction to The Doctor after he encounters an old friend of his who was assimilated by The Borg.