I have probably sunk something like 300 hours in org-mode and ultimately abandoned it in favor of a system incorporating Evernote and Nozbe. Org-mode has been a source of much frustration for me. It seems so great, it seems to have all the features one could ever want, but every time I've tried to implement it (three separate attempts, each time starting from scratch and thinking I knew "what I was doing wrong last time,") the system has grown huge and unweildly, leaky and unreliable, and missing key features that I needed.
On the plus side I learned how to use emacs really well.
edited to add: The iPhone app is pretty bad, for the following reasons: It is ugly and navigation is unintuitive, and the text-wrapping is essentially broken. Furthermore, you have to manually synchronize every little thing you do both pushing and pulling to your central repository or you'll quickly end up with inconsistencies which are a disproportionately huge pain to correct.
I actually still use org-mode if I'm simply going to be outlining a complicated project, but I've given up on using it as a task manager. I really wanted to like org-mode.
Late the party, and actually found this thread googling around for "Org-mode file/organization strategies." I've been using Org exclusively for work notes, and am finding myself in a similar situation re. being unwieldy. I constantly struggle with choosing one file per project, one big file with one headline per project, or files dedicated by type (one for todos, one for daily journal logs of experiments/efforts, references, etc.).
Org seems like it should be great for moving stuff around, but I find it not that easy. Refiling a mess of headlines ...
Several weeks ago, I began using personal wiki software Zim Wiki (free and cross-platform for Linux & Windows; I recommend nvALT on Mac OS X) to record all of my notes-to-self. I've found it to be a nice software tool for implementing some of the effectiveness advice I've read on Less Wrong. This post is a fairly personal overview of my usage.
I looked at a lot of personal information managers before choosing Zim. Here are the features that caused me to choose it over the other software I looked at:
Probably the most important feature: Jump-to-note capability with autocomplete. Pressing Control-J gives a text box. Start typing in the text box and it autocompletes with the names of any of the notes in my notebook (or allows me to create a new note). This is the proverbial 10% of the feature set that provides 90% of the benefit over scattered text files. Opening a specific note to add another thought or idea to it is a very common operation for me and this feature makes it very quick. Only a few tools I've found seem to have comparable functionality: WikidPad (with Control-O), and the Notational Velocity family of information managers kind of have it. (For Notational Velocity/nvALT, I recommend coming up with some kind of namespacing scheme so note names collide with note text less frequently in your searches. For example, I prepend reminders for future situations with "f.", journal notes with "j.", policy notes with "p.", Less Wrong post drafts with "l.", etc. Then command-L works as a pretty good "jump to note" shortcut.)
Pressing Control-D, then pressing return inserts a timestamp at the position of my cursor. This has been useful for a variety of logging-type applications. (I replicated the same thing with nvALT on OS X with aText.)
Zim is a desktop application. This has a couple advantages:
I configured a keyboard shortcut to open it, or bring it to the front if it was already open, using a modified version of the Linux shell script in this forum thread. (Alfred is nice for this on OS X.)
All my notes are stored as plain text files on my hard drive. I keep them under version control, which lets me do things like answer the question "what new ideas for becoming more effective have I had over the past week?" (I didn't use the built-in version control plugin because I found its UI glitchy.)
There's inter-note linking capability, also with an autocompletion dialogue. (Press Control-L to create a link.)
Moving through note browsing history can be done with Alt-Left and Alt-Right.
Using Zim has meant a really low level of friction for writing new stuff and retrieving/reading/adding to stuff I wrote. I've been using it about a month and I've got ~46K words in it, which seems to be around the length of a short novel. RescueTime says I use it 4-8 hours per week. Some stuff I'm using it for:
Strategizing. There's something kind of calming about writing my thoughts out when I'm choosing between several options or trying to figure out what to do. I suspect that as soon as the amount of information related to a decision exceeds the capacity of my working memory, I benefit from writing stuff down.
Logging stuff.
Writing therapy.
Recording business ideas, self-experimentation ideas, essay ideas, etc.
Making plans and filing away notes related to future circumstances.
Taking notes related to software I'm developing.
It's hard to measure how much benefit I'm getting out of all this, though it feels pretty useful. I'm inclined to agree with Paul Graham: