Any "advanced" text editor that can search directories should work: Notepad++,Vim,grep,... anything really.
I've been using a bunch of synced markdown files. Works for me, I just have a Markdown editor and a "grep-like" app for android. I'm not sure what you can do for iPhone though. When I've talked to people they couldn't seem to "browse for files/folders" which I thought was strange.
The one thing I'm missing is I'd like to "tag" my notes. I haven't decided how/if I'm going to do that yet.