Here's my list of the hardest thing I've had to do in all the games I've played 100%. I know some people may feel like they've had more trouble with other objectives, but these were the most frustrating parts of the games for me.
Banjo-Kazooie - Engine Room Jiggy
Banjo-Tooie - Cheato Page from Cloud Cuckoo Canary Mary
Conker's Bad Fur Day - Countdown
Donkey Kong 64 - Beetle Race in Angry Aztec
Super Mario Galaxy - Luigi's Purple Coins
Super Mario Galaxy - Grandmaster Galaxy The Perfect Run
Bonus: I know Diddy Kong Racing wasn't a platformer, but Greenwood Village Coin Challenge on Adventure 2 was probably one of the most frustrating and rewarding experiences I've ever had in gaming.
What's your list like?