If you like to input your thoughts into Wiki format, you would want to software like GTDTiddlyWiki or online service like PeanutButterWiki. However most of the Wiki system are web based (both online and offine), sometimes it may not handy to open your browser or even need to online. There is a open source software called wikidPad which should able to solve this problem:
wikidPad is a Wiki-like notebook for storing your thoughts, ideas, todo lists, contacts, or anything else you can think of to write down.
What makes wikidPad different from other notepad applications is the ease with which you can cross-link your information. Links in a wiki are created by typing in WikiWords. A WikiWord is any mixed case word typed into the editor. TodoList or JohnDoe are example WikiWords. The term wiki means “quick” in Hawaiian, and wikis are all about quickly linking your information together. Wikis are not a new concept, in fact there are many web based wiki servers available.
wikidPad is not a web server, or application server, or groupware solution. wikidPad is a standalone notepad like application, albeit notepad on steroids. wikidPad is like an IDE for your thoughts…