I have found what keeps my genealogy organized help's me find what I need whenever I want to make a trip to the Archives Library. I keep a folder just for this purpose. I will print out from my Family Tree Maker which line I would like to reasearch that day and put it in my folder along with large sticky notes and a small note pad. This way I can put whatever photocopies I make into my folder without them getting bent.
I also use a filing system, I read this when I first got started and have converted it a little to suit my needs. I have hanging folders with surename ancestry chart # on them. I keep all my documents in them, death records, Birth Records and a print out of the Family Group sheet and Individual sheet.
In three ring binders I have one for each surname that i use for my reasearch and just grab them with my folder to take with me when I do reseacrh. I put copies of records in these so I have them with me on a research adventure.
This is my first part of organizing my records.