Taker and Rock have good chemistry, but they both have many other guys they have better chemistry with. I thought their matches at KOTR, NWO, and the Raw match they had in 1998 were all at the very least good. They also had a match in 2000 that Taker ended up winning in the build up to Unforgiven, but I'd need to re-watch the match to judge it.
Taker and Austin had some odd chemistry. They had a couple of awesome matches (FL 99 and JD 01), but besides that their matches generally are very boring and uninteresting contests imo. Summerslam 1998 is very nostalgic for me, and it's a good match imo, but disappointing considering the hype and build up the match got. Their Over the Edge 99 match sucked from what I remember, the buried alive match was nothing special, and same thing for the Raw match in 99 where Austin won back the title. I know they had a PPV match in 1997 as well and a few matches around/before that, but can't say I really remember any of them.
Never thought Taker and HHH's chemistry to be honest was on the money either. I do think their WM17 and WM28 were excellent matches, as was the finish of the WWE Title EC in 2009, and the WM27 was very good, but to me, it just didn't feel like they meshed as well as they should've generally (of course the people that put the WM27 and WM28 matches at ****1/2+ each would disagree, but whatever). KOTR 02 was of course terrible, but the Raw match they had that year that HHH won and the UK PPV one I'm a fan of. Also the match between them on SD in 08 screamed mediocre, and I don't get why they'd put them in a random match on SD in the first place for their first match in 6 years.
Interestingly enough, if I'm not mistaken, Taker/HHH are among the only few matchup combinations to have matches featuring every face/heel dynamic. What I mean is they've had:
Face vs. Face matches (SD 08, WM27, AND WM28)
Face Taker vs. Heel HHH (WM17, Raw 02, and more I'm sure I'm forgetting)
Heel Taker vs. Face HHH (UK PPV in 02, KOTR 02)
and even the rare Heel vs. Heel combination (Raw 1999)
Not sure what other combination of wrestlers can claim they've done that, though most also haven't done heel vs. heel since they're so rare. I thought Taker/Angle may have fallen in the same category as they had a heel vs. heel match or two in 02, but they've never had a match to my recollection where Taker was the heel and Angle was the face.
I think Kane/Batista may have all the combinations as well. Heel vs. Heel (Raw in 04 where Eugene was GM... though I think it was short) and Face Kane vs. Heel Batista at Armageddon 2002. I'm not sure about the other combinations, but I'm certain face Batista vs. face/heel Kane has happened at some point, but not sure if both happened.