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I have the following requirements:

  1. 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.

  2. Minimally some form of markup, but ideally something I can drag and drop images into and do some formatting. Rich Text support is reasonable.

  3. Hierarchical organization, AKA outlining.

  4. 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.

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closed as off-topic by bwDraco, Kevin Panko, random Jan 19 '15 at 20:46

This question appears to be off-topic. The users who voted to close gave this specific reason:

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Tough question, looking forward to responses myself. All I ever wanted was something that combined the functionalities of Journler/MacJournal and OmniOutliner. – fideli Dec 30 '10 at 4:29
I don't want to add it as an answer, but I've seen that there's some mobile version/companion app for Circus Ponies Notebook. Maybe that's a possibility. Haven't used it for long, since I couldn't cope with its presentation (at least a few years ago, maybe that's changed). I remember it having formatting and cross-referencing; I'm not sure about outlining though. – Daniel Beck Dec 30 '10 at 18:55
You could add Yojimbo to the "no hierarchy" list of rejected apps :-) – Daniel Beck Dec 30 '10 at 18:56
And then there's Evernote. Haven't used it at all except for answering questions about it on SU, but for some reason, it's popular. Cross-platform, iPhone client, formatting, somewhat hierarchical. – Daniel Beck Dec 30 '10 at 18:57

Have you tried ShoveBox?

You can group your snippets by folder, but not into subfolders... I guess that's close?
Labels and Spotlight searching might fulfill your internal linking requirement.

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Thanks for the suggestion. I just checked it out and it's very similar to EagleFinder, with similar constraints. EagleFinder has the same structural limitations but at least has internal linking: you can drag a note into another and creates a link. – eatloaf Dec 30 '10 at 5:29

nvALT is what you're looking for. Best app I've used on any platform. It syncs to Simplenote, which makes it accessible anywhere. Or you can do Dropbox.

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Scrivener is mainly meant for managing actual writing projects, but could also be used as a note taking application.

  1. Syncs with Simplenote and apps that use Dropbox
  2. Documents are stored as rtfd, but it also has basic MultiMarkdown support
  3. Folders are the main way organize documents
  4. Supports links to other files
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If you're somewhat flexible on the outlining/hierarchy requirement, check out VoodooPad by Gus Mueller.

It's basically a personal wiki, and just like Mediawiki (Wikipedia) has some form of hierarchy through naming, you can do so here -- or use the "index" page to create your own, free-form outline: no need to use the internal list of pages at all.

If you don't mind breaking butterflies with wheels, check out the various editions of DEVONthink. I use Pro Office, and it supports a folder ("group") hierarchy of "files", which can be "rich text" i.e. notes with formatting, and those can be linked by Control-Dragging the target into the source document. You should get those features with the free DEVONnote (comparison).

There is an iOS client available, DEVONthink to go, but I haven't tried it. And there's a bonjour server sharing option, at least in the bigger editions, but I haven't tried that either.

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Thanks. Since my notes are mainly in TiddlyWiki and Tomboy, VoodooPad is a reasonable solution, despite the lack of hierarchy. And the developer seems to be active so that's a good sign. I looked at DevonThink/Note and it seemed to be no better than EagleFiler for my needs but with a lot of bells and whistles and a premium price. – eatloaf Dec 30 '10 at 18:40
@eatloaf You're welcome. Regular Dt -- the one with all the features you desire -- isn't that expensive at 50 US$ without discount, and the developer also likes these "bundle" deals that seem to be floating around regularly, at least for the regular edition. – Daniel Beck Dec 30 '10 at 18:52
I'll give DevonNotes another shot. I couldn't see how to accomplish those things on my first go. – eatloaf Dec 30 '10 at 19:19
@eatloaf I double-checked before I posted. Maybe I didn't understand your requirements fully? – Daniel Beck Dec 30 '10 at 20:22

OmniOutliner, from Omni Group, now has a mobile (iOS-7 and iPad only so far) version which is quite powerful. You can take notes, organize, structure, link, annotate and share with AirDrop.

The regular Notes app from OSX and iOS kind of work too. They're not as fancy as the other applications presented here, but they do the job. Outlining and markup are minimal, still you can add pictures and make hierarchical lists. And you can sync with iCloud or any other IMAP mail account. Notes app is missing the note linking capability though. The main advantage here is that it is free.

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