There are tons of outlining tools out there. Graphical ones, bulleted-list ones, physical ones the writer draws on large sheets of wallpaper, ones set up in word processor templates. Personally I tend towards onscreen sticky notes, maybe because of all the document review meetings I've sat through at the day job which included a "parking lot" full of yellow stickies. I've been using Tomboy Notes (available for Linux, Unix, Windows, and Mac OS X) since at least 2008, which is the last time I blogged about it.
Each note allows very basic word processor functionality, can be as long or as short as you like, and can be categorised into a notebook. Notebooks are just collections of notes given a label the user creates. It's a pretty unfussy way to store information, and if you forget what a note is called, the search function will let you do a text search, either on a specific notebook, all uncategorised notes, or all your notes.
I love Tomboy for outlining larger works of text. My Tuesday Serial has finally got far enough along that it's hard to remember all the character names and plot points, so I made a cluster of notes to keep track and illustrate this blog post at the same time:
If you look at the screen shot at full size (click to view), you'll see that all the major characters are have notes with their first names except for Beth Zondernaam. I was worried because I've had other characters named Beth in the past, so I changed the title of the note about her. Tomboy asked me if I wanted to update the links, and I said yes, so it did an automatic global search and replace for me. If a note gets deleted, all links to it get deleted as well (not the text itself, just the linking formatting and behaviour).
Notes may be exported to HTML. The links will stay intact, so if I were to export the top-level "Tilly with the Others" note, for instance, Tomboy would include all of the child notes attached to it. The result would be a single HTML page with internal links to the different notes (now sections in the overall HTML document). This has come in handy when I need to move content from one machine to another.
It is possible to synch notes (you can see that option in the menu screen shot), but I've never had much call to use it. Some of the features highlighted here can be altered or turned off as well.
Tomboy isn't as strict or as hierarchical as other outlining tools out there, but that's partly why I like it. I'll often arrange a set notes on a screen pane when I'm trying to organise something (there's that whiteboard parking lot training again). It doesn't go as far as some of the "mind cloud" organisers out there (which personally I see as a good thing), but the physical/spatial aspect can be a definite plus.