There are many different applications that may or may not be suitable fpr taking down your notes. Here, I will present a few, which I use myself, and yes, I do really use more than one of those apps since there are many different scenarios, in which I need to take notes.
Evernote
Evernote is a simple but really powerful application for note taking of any kind. Like any of these apps, it can be used to take notes in a text editor and to save them automatically. But, there is more to it. you can create screenshot notes, copy and paste notes via its menu bar item (a new note will be automatically created), and even create a kind of snapshot note, which will be taken via a webcam. You can tag you notes, and you can search via these tags or full text search.
But, the true power of Evernote lies in its web features. You can create an online account, which you sync your notes to. When synced, full text search can even be used on notes, which are screenshots or photos. To make this possible, Evernote applies a text recognition system to the imagefile on their servers, and after the next sync, its results are made available offline.
The Evernote desktop app comes to you for free, and even the online service is free, if you can manage with 40 megs of upload limit a month. If you need more, you need to pay a monthly fee. Versions of the
desktop applications are available for Mac and Windows, and there are also clients for different mobile phones.
Scrivener
This comes as the perfect app for the writer of long texts using a mac. It is Literature and Lattes application for writing anything longer than one page of text. But, its not only a writing application, but lets you manage your research for a larger writing project as well, and very efficiently as well. You can even add photos and pdfs to your research folder and have them always available in your research folder. If you are writing a longer text like a novel, or a scientific paper, you can use Scrivener to have your research notes stored in the same place and available in the same place as your actual writing project.
Scrivener can be bought for 39.95$ here, a 30 day trial version is also available. It is only available for the Apple Mac, no Windows version is planned. Highly recommended.
Journler
This is my place for taking down notes, that don’t go in any of those other apps. Its kind of a personal Wiki, where I can organize all my different shorter writing Projects. For instance, this blog entry was drafted in Journler. It can even be used as a simple GTD app, though I prefer Chandler for this. But it has all the tools needed for this, and is very easy to use. If you need a program to take notes of any kind in one place on your Mac, just use this. It lets you organize your notes in intelligent folders, insert photos, audio files and videos into your notes, and apply tags and full text search on them on the fly. It is a very powerful app, and if it wasn’t for the online features, Evernote would have to go. Journler is free for non-commercial use and available here only for the Mac.
Chandler
This is my GTD app, which I already introduced a few days ago, see here for my original blog entry. It is a great open source GTD and calendaring application, which even has great online features for free. It is available for Windows, Linux and Mac here. Very Highly recommended.
Well, quite a lot of useful apps for anyone to take notes. Feel free to comment, if you find any replacements, additions to these apps, which I might find interesting.

