Abstract / bottom line:
Markdown is over. ("Md is as if reading were an emergency situation.")
The challenge for note taking apps is: even if they see themselves primarily as editing apps, the first UX is about reading. (Reading first.)
Developers of markdown apps use an excuse: markdown allows a rendered external preview per page, but a reading experience without disruption is not provided. -- The truth about md is, this is not an excuse. It is a final verdict. 
Attempt 1: Desktop applications
Software users of the generation mobile may not know it. In my generation we all went through an absurd marathon of trying out desktop apps to find an application for managing notes :
Bento, Code Collector Pro, EagleFiler, Nottingham, Webnote, Yojimbo, TheHitList, Things, VoodooPad, TapForms etc.
And we went through a marathon of reading the relevant reviews. : - /
With the disappointing insight: using these apps would in any case result in more efford than benefit.
In my view the reasons to look for a note application are this:
- making links in the notes clickable/ tappable
(links between notes)
- displaying linked (local) images
- the ability to search and filter the files of the notes folder.
1. and 2. could obviously be done by Markdown. 3. can be done by SQLite or XML, e.g. the filtering system of the OS X Finder (Smart Folders).
But there was no desktop app that integrates these three points and leaves my notes as what they are (and should be): plain text files in folders.
The closest in 1 and 2 was Mou , the closest in 3 was Nottingham 3 (after it paused in 2013-2016 now Nottingham is maintained again).
Attempt 2: Blog software on localhost
My second trial to manage notes systematically was blog software.
In 2008 I installed Pebble – that are server-side generated blog pages (Pebble is still downloadable today but development is not active). - What I learned was this:
- To have installed (and to point to) the right JAVA version on a computer is not easy.
- To replace Apache Tomcat by GlassFish means to switch to a zero-conf solution. It simply worked.
- The full text search engine Lucene is really pro and works well.
- But since my blog is not for commenting it is overdone to have server-side generated pages. -- In the end my writing was too slow (and how I managed my notes) and I gave up.
- Pelican's templating system Jinja is really advanced. To have no database or server-side logic frees from dependencies.
- But as the final result I asked myself: for what purpose do I use a blog software at all? -- Actually I do not need an "engine" at all.
Pelican/ Markdown was:
- for my note taking not simple enough. - Even to have two files for one note (to generate HTML from Markdown) is one step too many. Not to mention you have to regenerate the whole category lists each time (when you want to have database-like behaviour).
- for my blogging too simplifying. - In my postings I play with CSS, SVG and graphical experiments.
- Markdown is great with apps like Mou, where you can have editing mode and the rendered result at once. For writing in chats it is perfect. -- But for essay writing I don't need the extra layer of abstraction markdown provides. I have in mind anyway what HTML syntax will be generated when writing markdown.
3. The solution I use now (and I'm pleased with): Pinboard.in
In 2011 I checked the web service Pinboard.in for tagged bookmarks and notes. With Pinboard especially searching and filtering works in a very convincing way.
Also the most usefull desktop tool for Pinboard bookmark collections is nearly perfect: Little Bookmark Box (LBB). (for iOS : Pushpin)
Since then Pinboard/ LBB are my most frequently used apps (after Finder, web browser and BBEdit ).
The apps can be used for noting down addresses, phone numbers, lists of (clickable) URLs in the notes field, personal comments etc.
The Little Bookmark Box makes use of the filtering system of OS X (Smart Folders) for filtering the notes/ bookmarks by tags, title, text strings etc. (including boolean).
For example I can find entries that are accidentally tagged with invisible tags only (tag names starting with period) and not with regular tags:
Most important for using the filtering system is to add top-level filters
by holding down the
alt key when clicking the plus icon (the plus icon turns into a
4. The solution I once dreamed of: md + SQLite
When you want to bookmark URLs it is obviously the best choice to use a web sevice. And for note taking the best is most likely an offline application. -- The following list may be quite unrealistic, but I would say: let's put the best parts from solutions together I've already mentioned here (see  ):
- Note app as a desktop application that works offline
- Notes as plain text files in folders (of the device's file system):
.md .txt .html (poss.)
- Browse mode: integrated render engine that provides working links between local pages for local browsing  and that displays (basic-) formatted text .
- Edit mode: writing in md files with features as the Mou app provides it
- List mode: tagging, filtering, searching of entries as the LBB app provides it (SQLite).
In terms of the mentioned applications the ideal app could be described as if it were:
- "Nottingham with ability to browse the rendered views"
- "Mou with ability to index and filter files via SQLite"
- "LBB with ability to edit markdown in a large note panel".
- "Coda for locally used markdown notes"
It would not only be perfect for notes and bookmarks. It could be used by writers/ journalists as a md/ writing environment with focus on local indexing and tagging - for those who prefer simple hand coding/ writing instead of a fat CMS.
A web/md text editor with focus on the browse mode -- using, viewing, searching, listing the own (rendered) pages locally. 
5. Tech tips: Exporting bookmarks
- Saving bookmarks in Little Bookmark Box and uploading them to Pinboard.in is the wrong way because LBB doesn't support hard line breaks in the note field. (It doesn't support the multi-line view of the large Pinboard note field.)
If you don't want to relinquish hard line breaks the export has to go the other way round from Pinboard to LBB.
- It takes only a few seconds to export 1,000 bookmarks as a Netscape HTML file from Pinboard into LBB.
Since I use in LBB only Smart Boxes (the only standard Box is the imported file) there are no further steps, it just works. The configured Smart Boxes in LBB survive when I delete all bookmarks before importing a new complete set from Pinboard.
- Webnote as an alternative to LBB (with the advantage of having a real note field) is focused on Delicious and isn't maintained anymore (v2.0.0b44).
- XBEL as an exchange format does not support tags.
The "ancient" Netscape format works well between Pinboard and LBB.
- If you use Pinboard as a social tool it may be usefull to have a lot of distinct tags. -- I prefer to use tags not for finding a note but to get a clear outline (tag cloud) of my site, with only a few distinct tags. To find a note afterwards –let's say for the topic 'genetics'– I simply write in the keyword 'genetics' in the note field (without making it a tag). -- The tag is 'science'.
- You should keep your
pinboard-export-yyyymmdd.htmlfiles. They are perfect backups: simple-structured, readable by humans and any appropriate app.
6. Criticism: Syntax of web page titles
There was a time when page titles (from some exemplary web sites) looked like this:
The syntax was systematical, informative and readable for humans. And it was lucid in bookmark lists. -- This is all gone now and sacrificed for SEO. Nowadays titles look like this:
..malformed and a demise. -- The title should start with the topic, the news, with that what I'm searching for. The origin of a web page should be separated in the title. A separator is not something that looks like a letter, like
: . It has to be cross, obstructive in the reading flow. The only character that is more obstructive than minus is double minus (and that would be overdone). – To put it another way:
- within the topic part should be avoided.
 added 2015-09 : It was a hype in 2011/ 2012 to use static website generators instead of database-driven sites. OctoPress (jekyll) on GitHub and Pelican on Heroku were typical constellations. It was a chance for developers to show how cool blog posting on the go can be.
In fact writing isn't that easy and fast. I do not need postings on the go and site generators.
 added 2015-09 : A web render engine/ browser that recognizes markdown is still not there (browsers are for tasks only that are more complicated).
Mou.app solves the problem by opening a new document's window when a link is clicked (a new tab would be better).
Coda for iOS (launched 2015-07) provides a http server on localhost and the ability to browse local pages (an unrecognized really big step forward on iOS devices). But for md browsing is unsolved, there is no implemented UX. A somewhat browser-like experience would have saved markdown.
 added 2015-09 : I know, it doesn't work with markdown. - Even a neat note app like Nebulous Notes misses (when it comes to markdown) what the purpose of note taking actually is. -- Notes are not there to be written down but to be read and used.
The web is clearly different from note taking. There we have (still) a division: browsers are for reading and editors are for writing. -- Not so with note apps. Note apps do both and apps that use md should provide a priority switch in the settings (and should make switching fast and easy): reading first / writing first. (And in reading-first mode we should have on the bottom of the screen a button 'Edit' instead of 'Render Markdown'.)
To check out Nebulous Notes I uploaded my good old (and long)
single-file-address-book.md. It works well (thanks to the # anchor jump feature of the md renderer) und it looks as it should (thanks to the personalizable css in NN). -- But when I want to use it, before I get to the rendered view of my address book I'm always confusingly confronted first with things I've recently done under the hood (writing). As if reading were an emergency situation.
The objection "If you primarily want to read your final document, go generate html from your md and use a browser, period" misses the point.
When my final target is html and a web browser then I write html (markdown doesn't work well for that, see above). When I have to note down something I would not write html (html doesn't work well for that, see above). But I would expect the convenience anyway my notes are nicely readable in a note app.
To be honest, the html advice is just what I observe now. When I write I write html (on a desktop) and when I note down a little note I stay with .txt (resp. pinboard.in ). I will not write md again until a md app is able to browse throughout all my notes in render mode and is able to provide filtered lists for reading. (Reading first.) – To put it another way: I will use md never again.
My decision also helps in the case of Nebulous Notes: when staying with .txt reading and writing have the same UI. Web links are still tappable, the app is well designed and I enjoy using it.
For everithing else (that is larger than a few words and that is for long-term usage) I write HTML (even though viewing html on localhost of the coda app is not exactly comfortable up to now).
Trailing a summary of what I experienced in NN (issues are mostly not NN but system or md issues):
- In markdown-landscape mode the top and bottom nav bars do not hide when reading/ scrolling down. - On small screens another reason not to use markdown.
- In markdown there is no syntax for formatting mail addresses when they are long. - That can lead to unwanted extended page width (overflow)
(but to insert html instead within markdown works)
- In markdown there is no way to disable it when all kinds of numbers or street names in the text are interpreted as linked events (map, calendar).
- No reading-first mode
- (everything else is fine, as of version 8.4).
 added 2015-09 : Apple implements the features I once was waiting for with it's new Notes app for iOS and Notes app for Mac OS X . -- But anyway, I would refuse to throw my data into that sort of OS-dependent-Rich-Text nirvana land.
[ Addition two days later: Above I mentioned that NN notes and Pinboard (backup files) stay human-readable. - But when I come to consider it, files of plain text are not human-readable. So I should refuse rather "to throw my thoughts into a wall-outlet-dependent-text-program device". -- Mankind didn't experience yet how it feels when text programs suddenly don't work anymore in case of cyberwarfare. ]
 added 2015-09 : It's odd, I checked out the notes feature of Pinboard.in (
notes.pinboard.in) some years ago. The notes are markdown-formatted, work well and easy, have even a URL. But –I don't know why– I don't use it. — That's saying a lot about the whole topic. Markdown is over.