Winning Le Mans overall is the greatest achievement in sports car racing, no question about that. But how about the class/overall victories in lower classes, how do you rank them? Below how I'd rank them.
GTE-Pro at Le Mans:
This is the class with the most serious manufacturer involvement after LMP1 and Le Mans class victory is the greatest prize in it.
Overall at Nürburgring/Spa (GT3):
GT3 is a class with lots of involvement from a huge variety of manufacturers. Even though these are overall victories, I don't put these on the level of Le Mans GTE-Pro victory; GTE is still the higher priority for manufacturers. I can't choose which of these I place higher; Nordschleife is the ultimate challenge as a track whereas Spa has more manufacturers represented.
Overall at Daytona/Sebring (DPi/LMP2), GTLM at Daytona/Sebring (DPi/LMP2):
Rolex 24 and Sebring 12h surely have great heritage but I just don't rate those victories on the level of Nürburgring/Spa. That's partly because you have the best talent divided in multiple classes in those Florida races. DPis may be the fastest prototypes behind LMP1s but in terms of OEM involvement the class is behind GTE and GT3. GTLM may be only the third-fastest class but it's got the greatest OEM involvement, that's why I rate the GTLM class victory on the level of the overall victory in those races.
Of course, if a GTLM car won the overall in IMSA like Porsche did at PLM '15, I'd put it even above a Le Mans class victory.
LMP2 at Le Mans:
This is below Daytona/Sebring victories because it's not for overall, you don't race against manufacturer DPis, and you have pro-am crews.
GTD at Daytona/Sebring (GT3), GTE-Pro at Le Mans:
Can't really put either pro-am GT class victory above the other. Le Mans is the bigger race but I rate IMSA GTD as a class above WEC GTE-Pro. While GTD is a pro-am class, that's where GT3 manufacturers like Merc, Audi, and Acura get to the biggest stage in American sports car racing, and I think it's the better class in terms of driver talent.
I'm not going further, those are the main achievements in those classes.