I have been using a piece of software (for Macintosh) over the last six months or so which I have really come to depend on. I have just realized how often I now use this that I wanted to recommend it to others. It is called VoodooPad. It is basically a kind of offline Wiki (although it supports communication with an online wiki) or you can think of it as a kind of “document database.” Basically, if you are a completely disorganized person, like me, and you have lots of little snippets of information (links, dates, lists, notes, etc.) then you can use VoodooPad to keep it all “linked” together in one little file that is easy to backup.
Basically you type in the VoodooPad ($20, or free Lite version) notebook and create a new document by putting two words together and making it a “link” which automatically creates a blank document in VoodooPad. You can then create more links within that document to new documents and so on. The new documents can open in a new window or in the same window (kinda like a document “browser”). You can also drag web links into the pad (which open a browser when you click on them) or files (which open the file when you click on its link). I first found this useful when preparing for my PhD applications. I made a “link” for “PHDNotes” and then a link for each school I was looking into, then each professor, department, or various categories of information about the application process. It was then easy to add tons of information within any of these while still having it all kind of “naturally” organized like a Wiki website might be. Of course, you can search through all your documents at once and export data in various formats. For a person like me, either I dump stuff like this in dozens of files and never remember what goes where, or I tend to dump everything into one file which is really a pain to sift through.
The excellent HogBay Notebook has wiki features built in as well.
I’ve installed a local copy of MediaWiki on my mac and run it as localhost so I can access it from any browser even if I’m offline. This allows me to keep my bookmarks independent of any particular web browser. It also allows me to work on wiki pages before I post them online to wiki.oxus.net which uses the same software. This isn’t quite as quick and easy as using VoodooPad, but I like the platform independence. Its also free.
Hog Bay is a decent program too, but I prefer OmniOutliner for my notes/outlines and VoodooPad for wiki style scrap notes. I often drag omnioutliner files into VoodooPad for quick access to my outline files.
Running a wiki local is a good idea too.
The new documents can open in a new window or in the same window (kinda like a document “browser”).