For many years I have kept a personal diary, first written in longhand, later typed, and, currently, composed in my computer's word processing program and stored on a floppy disk.
As time passed and I have been able to devote more time to genealogy, I found myself writing about it quite a lot, inserting notes and comments in among the paragraphs about other aspects of my daily life. Then, too, there were those scraps of paper with references to people and agencies I have been in touch with, ideas for new search strategies, and who knows what, all floating around, tacked to the bulletin board, or hidden under other scraps.
About a year ago it occurred to me to start a separate "journal" on my computer just for my genealogical research. When I send off for, or receive, a vital record, query another researcher on a particular surname, have a sudden insight, or feel triumphant over a new discovery, it goes in this journal. Family names are bold faced, so I can refer back to them more easily. And I do refer back -- in this way the journal helps me remember what I've been working on. (We all jump around from one surname to another, don't we?)
My struggles with organization are noted here as well. Just the act of writing out thoughts helps solve many problems, at least for me. Possible solutions to thorny questions have been known to rise to the surface when they were set down in black and white. Or, seen in the light of day, a particular issue may recede into the background or vanish altogether because its insignificance becomes obvious. (Why should I care about Great-uncle Jacob's third wife's sister-in-law? How did I get that far off-topic anyway?)
The ongoing research journal could be considered a kind of confessional and as well as a progress report. There are certainly more organized ways to keep this information, with tables, logs, and lists of various kinds, but right now this seems to work best for me. If you have suggestions or comments, I would be happy to hear them.