I tried many, cloud apps, desktop apps, wikis. But in the end, I was never comfortable with putting all my thoughts in documents in a weird format (at best) or in the cloud (at worst). And most apps didn't offer any huge advantage to compensate for that.
I have backups of my notes folder. I can grep through it when I'm looking for something. I can edit it from any computer. And I know it will still be readable in 10 years.