I used to use Journler for taking notes on my computer, and when Journler died I moved on to MacJournal. However, nowadays I constantly find myself using different computers (Mac, Windows, Linux) and various mobile devices (iOS and Android) every day, and have found it to be problematic to be locked into an OSX/iOS application for note taking/access. There are some cross-platform note-taking applications out there, most notably Evernote, which I have tried to become friends with several times, without success. My biggest problem with Evernote is that it locks you into their system, and you cannot export everything in your library in an easy way.
Inspired by a blog post by Alex Payne, I have decided to change my note taking to the simplest and probably most future proof system: plain text files in folders. All OSes that I know of can handle text files and folders without problems (at least if you are a little careful with file naming), and you can also search your files using standard built-in OS search functionality. So there is really no reason for using a dedicated application for this.
Fortunately, MacJournal let me export my entire library as separate RTF files, and I wrote a little script that added the creation date of each note to the beginning of the file name. So now I have a folder called “Notes” with all my notes from the last 7 years as separate RTF files, organized after creation date.
For new notes, however, I don’t even want to use RTF files. I have had some bad experiences with opening RTF files in different software. Since I am often moving files between MS Word, OpenOffice Writer, TextEdit, Bean, etc., there is always something being messed up (particularly bullet lists). Instead, to keep some richness in the texts, I am now writing notes using MultiMarkdown. I have been doing this for a month’s time now, and think it works great, even though it adds a little overhead in terms of the formatting. However, the freedom to easily export the files to HTML, LaTeX and RTF later on makes it less of pain overall. And storing the notes using Wuala makes it possible for me to access them on all my devices and computers.