-Eliminate Dragonite and Tyranitar; they can be Hatched or walked at 5km/candy, and can be attained via research quests. Those are much better ways to get candies for them.
-Ho-Oh is not currently useful enough to spend rare candies on. (Which makes me cringe as I've got 3 93%+ Ho-Oh's I want to power up, but...)
-Groudon is... nice, but not particularly useful right now. It might be a good place to "dump" excess Rare Candies, though.
-Kyogre is also very nice, but not exceptionally useful right now. Like Groudon, it might be a good place to "dump" excess Rare Candies.
-15/15/10 Mewtwo w/Shadow Ball is very nice. Having multiple Mewtwo's with Shadow Ball powered up is likely going to be a great investment no matter what. Like Kyogre and Groudon, it's not a bad place to "dump" Rare Candies either.
That leaves... Rayquaza. Attack 15 Rayquaza is going to be useful in the next few months (assuming the other Gen 4 Dragons come out), so I would suggest using the Breakpoint Calculator on this site to figure out how high you need to raise Rayquaza to get the most use of if it during those raids. Then use those Rare Candies to power that one up as much as you need to.