I have the following requirements:
Mobile accessibility: Either a complimentary iphone app to sync with, or DropBox or Google Docs syncing or equivalent so I can use other mobile note applications to edit notes remotely.
Minimally some form of markup, but ideally something I can drag and drop images into and do some formatting. Rich Text support is reasonable.
Hierarchical organization, AKA outlining.
Internal linking (note to note). I like to cross reference items and thoughts internally and the relationships aren't always hierarchical.
These were closest to what I was looking for but, as far as I can tell, suffer from the noted flaws:
VoodooPad : No hierarchy. I like that it uses plain text for links instead of a hashed value. The frontrunner solution.
Mori : No mobile solution.
EagleFiler : No item hierarchy.
MacJournal : No entry hierarchy. iphone app converts edited entries to plain text.
Evernote : No interior linking. No hierarchy.
I think I've tried every serious contender and none of them have all four (seemingly simple) requirements. I'm hoping that I'm either missing an existing feature in an app I've tried or that someone knows of something I haven't found it yet.