Extra time

Level 1: An enormous help! 10/10

Level 2: Could be useful in higher levels. 8/10

Level 3: Still Useful. 7/10

Extra arrow

Level 1: Rarely helps, because the direction of the arrow is purely random. 5/10

Level 2: Helps a little more. 6/10

Level 3: Helps a little.  7/10

Furtive Option

Level 1: Snuggy is faster and can run past bombs more than once.  Pretty useless. 4/10

Recycling

Level 1: Useful!  If you're stuck, you get a new puzzle and the timer is reset. 9/10

Level 2: Still useful, if you didn't get the solution the secont time around. 8/10

Level 3: If you can't figure it out by now... 7/10

Tiny Plier

Level 1: One object is taken away at random.  That's it! 1/10

Level 2: Still useless.  Do not buy this! 1/10

Level 3: Marginally more useful, but still... 2/10

Divine Help

Level 1: Tells you where to put 1 arrow.  Rarely helps. 4/10

Level 2: Could be useful. 5/10

Level 3: Gives you three hints, which could help... 6/10

Unlimited Katanas

Level 1: Put down as many swords as you want, allowing you to destroy all bushes.  Cool! 8/10

Survival instinct

Level 1: Snuggy turns around if he were to reach the edge.   Not often useful. 5/10

Super Bag

Level 1: Being able to select 4 options can be handy. 6/10

Level 2: But you don't really need 5 options. 5/10

Level 3: And you definitely don't need 6 options. 4/10

If I were to choose three, I would choose the following:
Extra time Level 1, Recycling Level 1, Extra time Level 2