Here we go...funny I thought deciding NTSC would be harder, but it wasn't. I reached the same top-3 as you ScouB. On PAL there are several worthy candidates, whatever you pick it feels unfair.

NTSC
1- VL2 45"99 (unexpected barrier breaker, crazy race on crazy course. May be my best 5-lap)
2- MC2 11"12 (very special because of all the super advanced strats invented to get there, just insane)
3- DP1 1'07"82 (I would have stopped at 1'07"9x if I even got there at all. True 5-lap mastery!)
PAL
1- MC2 12"02 (1 of the most shocking WR chronos in my memory, the gap to #2 makes it mythical)
2- VL2 8"69 (finally a video of the cursed WR, possibly my hardest worked for PR of all time. 8"8x laps looks sick already!)
3- DP1 13"59 (I was really hesitating between this and the 5-lap, but 13"67 was already close to maxed and no strat change was done to get into 13"5x, WTF!?)
ScouB and me seem to agree for the most part about which ones are special. I would also mention the MC2 5-lap, it's the biggest WR gap in modern times and I can imagine it's super hard to be consistent enough with that funky strategy. I would also make a mention of DP2 16"25, which surprised me a lot, as the 16"26 of last year looked so bloody perfect already.
The orders are more or less random for me too, they could be different if you ask me again tomorrow.