Zelda: Ocarina of Time
I've beaten the main story in about 2 months, but I was stuck at 90 skulltula tokens for years. It took me long to figure out you had to free bugs above a magic bean spot to get a skulltula to come out. I quickly got 100% completion after that.
Zelda: Majora's Mask
It was much easier to get 100% completion in this one. The main story took me 2 weeks or so and gathering all masks, pieces of heart, notebook notes and equipment upgrades took me a couple of months.
Golden Sun 2
Gathering all the djinns was quite diffecult and beating Dullahan to get the last summon was just insane. I think it also took me a few months to get this game to 100%.
Donkey Kong 64
Took me months as well. All the worlds were simply huge, making it very diffecult to find all the stuff that you can collect.
Super Mario 64
Probably a year to get all 120 stars.
That's about it. Of all the games that I have, Final Fantasy VIII is now the closest to 100% completion. I just need to get a few more cards from the card queen.