Sets actually named on cards:
Exact references:
Alliances (Unlikely Alliance)
Visions (Vision Charm)
Weatherlight (Skyship Weatherlight)
Stronghold (Volrath's Stronghold)
Urza's Legacy (Legacy Weapon)
Judgment (Dominaria's Judgment)
Legions (Sliver Legion)
Mirrodin (Mirrodin's Core)
Darksteel (several)
Fifth Dawn (All Sun's Dawn)
Coldsnap (Cold Snap)
Time Spiral (Time Spiral)
Future Sight (Future Sight)
Conflux (Conflux)
Worldwake (Nissa, Worldwaker)
Avacyn Restored (Avacyn, Angel of Hope)
Fate Reforged (Crux of Fate)
Oath of the Gatewatch (Oath of cycle, Call the Gatewatch)

Close in concept:
Fallen Empires (Sarpadian Empires Vol. VII)
Invasion (Invasion Plans, ahead of time in Stronghold)
Mercadian Masques (Unmask)
Planeshift (Planar Overlay)
Apocalypse (ahead of time in Tempest)
Scourge (Scourge of Kher Ridges, stretching, but pretty sure it is a reference)
Betrayers of Kamigawa (Night of Soul's Betrayal)
Ravnica (Soul of Ravnica)
Guildpact (Seal of the Guildpact, and a few others)
Morningtide (Maralen of the Mornsong)
Eventide (Enchanted Evening)
Shards of Alara (Shard Convergence, among others)
Alara Reborn (Child of Alara)
Zendikar (Soul of Zendikar)
New Phyrexia (Soul of New Phyrexia)
Innistrad (Soul of Innistrad)
Return to Ravnica (Deja Vu)
Gatecrash (Ogre Gatecrasher)
Dragon's Maze (Maze's End)
Theros (Soul of Theros)
Born of the Gods (Nyxborn creature cycle)
Journey Into Nyx (Starfield of Nyx)
Shadows Over Innistrad (Shadows of the Past)

COincidental:
Mirage (Convincing/Lingering/Shimmering Mirage)
Tempest (several cards, Shu Yun, the Silent Tempest being the funniest)
Nemesis (True-Name, and several others)
Prophecy (in Homelands, one of the coolest bad cards ever)
Torment (in Stronghold)
Onslaught (in Exodus)
Dissension (in the Ranks, in Shadows over Innistrad)
Planar Chaos (in Judgment)
Morningtide (in Torment, of all places?!)