I'm pretty-much with imagine gaming on this one; I name everything, and I name it consistently (at least I try). I do this on the basis that if someone else looks at my code, they should know what's going on without too much trouble, and if I look at my code in 6 months, I should also know what is going on!
I tend not to create many comments, because well-organised and well-named code shouldn't need much in the way of comments.
When I wrote my book, I kept a spreadsheet which kept track of all the actors, scenes, behaviors, etc and although it required extra effort, it made life much easier in the long-run. I'd definitely recommend doing that for larger projects. Actually, it's something I would like to see Stencyl do automatically. Easier said than done, I know, but it would be great if Stencyl could create some kind of diagram or table automatically. For example, if I selected a scene, it could list all the actors and behaviors linked to that scene.