As the others said, Ocarina of Time and Majora's Mask were the only games with time travel.
OoT(Ocarina of time) - You can travel forward and back by 7 years, but there's no point system.
MM(Majora's Mask) - Had a three day cycle where similar to OoT, you could travle through time to complete specific tasks, but, you could get rewarded with items. But other than that it had no point system
Zelda 2 - Had a point system but no time travel
FS(four Swords) - had a point system after each map but no time travel. I think Four Swords Adventures was the same in the multiplayer campaign.
Also, there were a couple of non canon games that also had point systems.