
"Valkyrie Dimension" Challenge. Considered the hardest DDR song for the longest time.
https://www.youtube.com/watch?v=Hromx6HeN_w
"Egoism 440" Challenge. 440 refers to the average tempo and there's 16th notes towards the end.
https://www.youtube.com/watch?v=l7Vx5FvX7-E
"Over the Period" Challenge. Those slowdowns are insane and make the Pluto series look reasonable.
https://www.youtube.com/watch?v=YKQX0kgiNtI
"Soulless 6" (Exilelord). It's a Guitar Hero 3 custom originally but even the bots can't FC parts of this.
https://www.youtube.com/watch?v=5gMspNaL2S0
"Paradoxx" (D28)
https://www.youtube.com/watch?v=rquLGNHuxvI
"Bemera" D28. One of the most infamous songs in Pump It Up history.
https://www.youtube.com/watch?v=SExxVYHfMGs
"Vertex 2" Expert. Possibly the hardest song in In The Groove.
https://www.youtube.com/watch?v=16b5dp748Eo
"Mendes" Black Another. It's crazy even by Beatmania IDDX standards. Total notes in two minutes, 2626 (on Black Another) or 1831 (on Another).
https://www.youtube.com/watch?v=Y57snv0G0TI
"Mei" Another. Possibly the craziest and most infamous Beatmania IDDX song on Another (the highest normal difficulty). Exactly 2000 notes in a little over 2 minutes.
https://www.youtube.com/watch?v=yW34iG4bsQw
"Operation Ground and Pound" by Dragonforce Expert (Rock band 3 chart). It's freakishly overcharted and it's DragonForce. Nuff said.
https://www.youtube.com/watch?v=jIS52CW3Gdg
Edit: Added "Soulless 2: Mechanical Machines" (GH3) by ExileLord. It's been 7 years and there still isn't a legitimate FC.
https://www.youtube.com/watch?v=_-fy2FsFDiM
"Dystopia" by Chaotrope Expert. Chaotrope (creator of some of the hardest RBN songs) said this is possibly his craziest song.
https://www.youtube.com/watch?v=WuQJ8_CRL70
"Cypher Gates" MX. Considered one of the hardest songs in DJMax Technika for good reason.
https://www.youtube.com/watch?v=NJ8hle83ZF0
"Xeus" MX. See "Cypher Gates".
https://www.youtube.com/watch?v=xxlU0vW0JbA&t=2s
FOF songs that deserve mention include; Francesco Fareri - "Suspension" (sean2490), "Dark Matter" by Rusty Cooley (Puppetz Hero 4), and "Soul of a Robot".
Maybe you guys got a choice that isn't there ...

Edit: Added reasons why explainations for these difficult songs (on most of them anyway) and an ITG example.