Mercy's old ult, obviously!
Joking. Every ult can be countered in some way, shape, or form. 76, Reaper, D.Va, or really any non-CC or protective ult can THEORETICALLY wipe an entire team out. It's seriously situational and depends a lot on what is going on and both team comps, but anything is possible.
But personally, I consider ults that help your team way more beneficial than STRICTLY (Valk allows Mercy better pew pews, and Grav does damage, but that's not their focus) damaging ults. And among your team centric ults, I'd say Lucio. It can be used to survive other ults, escape, initiate, or even USING IT ON YOURSELF TO SOLO TANKS. It's the Swiss army knife of ults. Plus, it isn't DIRECTLY countered by other ability except bullets and projectiles.
Totally not biased Zen main saying his is the best, but it does have a direct counter in the form of Ana. It's still a fantastic ultimate, just I rate Lucio's higher.
Something I don't see people talk about is Ana. It's not the best, but nano-ing someone at the right moment can win games. Nothing ever beats the good old NanoGenji=Profit.
EMP shuts down any chance at using abilities. It's a hard ult to use properly, but it's just a big middle finger to the enemy team. Getting into higher levels has made me appreciate it more, before I thought it useless, but it saves my ass from having to use Transcendence a lot of the time.
Obviously, I think really it comes down to preference. I just seem to get the most value out of correct usage of DROP DA BEAT, RIBBIT WOOOOO than anything else.