If you're going for a 100% playthrough of the game, here's what I've got. I've played through the Hero Mode and gotten just about everything I possibly can AFAIK and defeated the final boss. There is nothing else that I can do in the game except maybe find a few Sheikah Stones hiding off somewhere or some missing Goddess Walls.
WARNING: *SPOILERS* AHEAD
First of all in the Collection page of your inventory, you should have everything in the purple section checked off.
- You should have delivered Cawlin's letter.
- You should have done something about Beedle's missing bug.
- You should have retrieved the missing Rattle.
- You should have gotten all Gratitude Crystals (there's 80) to Batreaux and turned him into a human.
Then in the main Gear page, here's everything starting from the left.
- You should have the Master Sword with all 3 flames:
- Top: Din's Flame
- Right: Farore's Flame
- Left: Nayru's Flame
- You should have found all the Pieces of Heart in the game. It should appear as a full heart and not empty or partially filled. Without the 2 Life Medals equipped, you should have 18 Hearts at the end of the game for a grand total of 20 Hearts.
- You should have the Tycoon Wallet given to you by Batreaux with 3 Extra Wallets (giving 900 Rupee capacity) purchased from Beedle.
- You should have 8 Dowsing slots total with 6 of them filled:
- Top-Left: Rupees
- Top-Right: Treasure
- Right: Hearts
- Bottom-Right: Goddess Cubes
- Bottom: Look Around
- Bottom-Left: Gratitude Crystals
- You should have 8 slots available in your Pouch.
- You should have 8 Items total in their upgraded forms:
- Top-Left: Gust Bellows
- Top: Sacred Bow (2 upgrades)
- Top-Right: Bomb Bag
- Right: Tough Beetle (2 upgrades)
- Bottom-Right: Big Bug Net (1 upgrade)
- Bottom: Scattershot (1 upgrade)
- Bottom-Left: Clawshots
- Left: Whip
- You should have the fully assembled Triforce.
- You should have the Stone of Trials.
- You should have the Goddess Harp with all 5 songs:
- Top: Song of the Hero
- Right: Farore's Courage
- Bottom-Right: Din's Power
- Bottom-Left: Nayru's Wisdom
- Left: Ballad of the Goddess
- You should have the Sailcloth.
- You should have the Water Dragon's Scale.
- You should have the Fireshield Earrings.
- You should have the Mogma Mitts.
Finally, for the items:
- You should have 5 Bottles.
- You should have a Braced Shield (2 upgrades)
- You should have a Fortified Shield (2 upgrades)
- You should have a Goddess Shield (2 upgrades)
- You should have the Hylian Shield*
- You should have a Large Seed Satchel.
- You should have a Large Bomb Bag.
- You should have a Large Quiver.
- You should have 2 Life Medals.
- You should have 2 Heart Medals.
- You should have 2 Rupee Medals.
- You should have 1 Treasure Medal.
- You should have 1 Cursed Medal.
- You should have 1 Potion Medal.
- You should have 1 Bug Medal.
* I actually don't have the Hylian Shield, getting it in Hero Mode is TOUGH!
Some other things worth noting:
- The Goddess Statue should now be on the surface at the Sealed Grounds.
- Beedle's shop should be completely sold out.
- You should see Batreaux in human form at the Bazaar during the day.
- The Pumpkin Pull should be available to you in front of the Sparring Hall after helping Fledge.
- Dodoh's High Dive should be available to you at Fun Fun Island after helping Dodoh.
- Bug Heaven should be available at Bug Rock.
- Clean Cut should be available at Bamboo Island.
- Thrill Digger should be available at Eldin Volcano.
- Rickety Coaster should be available at Lanyru Desert at the Shipyard.
- The Thunder Dragon's Lighting Round should be available at Lanyru Desert at the Lanyru Gorge.
That's about it. I'm pretty sure this is everything there is in the game.