I use notebooks for the little bit of note taking I do. I like it because it has quite a decent range of sync options, including via WebDav which is what I use with my mac. Edit on any device/PC and sync to the iPad before and after I use it.
I'm really not keen on any app that requires use of a non self hosted cloud. I'd rather host my own for the majority of my private documents and have the cloud as an optional extra for when I want something either public or to be shared with co-workers.
It's far from my idea of an ideal app, but it's usable, simple and works, which is what counts