Joplin - Joplin is a free, open source note taking and to-do application, which can handle a large number of notes organised into notebooks. The notes are searchable, tagged and modified either from the applications directly or from your own text editor.

EagleData - Freeware database for Mac

OneNote - Get the OneNote app for free on your tablet, phone, and computer, so you can capture your ideas and to-do lists in one place wherever you are. Or try OneNote with Office for free.

Zim Wiki - Zim is a graphical text editor used to maintain a collection of wiki pages. Each page can contain links to other pages, simple formatting and images.

CherryTree - A hierarchical note taking application, featuring rich text and syntax highlighting, storing data in a single xml or sqlite file.

TiddlyWiki - a non-linear personal web notebook