CrazyMike:
Bear in mind, I'm only a technician, but I'm working with an aim of going back to school, so when I started building my organizational system, I tried to take that into account. Also, my PI expects much of the same of me as he does of any other student or postdoc in his lab - I have to go to the local seminars, know about all the labs projects, etc. I'm also taking free courses for a Masters in Clinical Research (free because I work for the medical school, and I can only earn a maximum of 10 hours credit in 2 years, so it's not THAT great). So you can probably glean something useful out of it.

I made my Cornell Notes pdfs myself, I have lined, gridded, and blank pages, depending on what kind of notes I'm taking. The top margin covers the entire width of the paper, and is 1 inch deep. The next 8 inches is divided into 3 columns: 2.5 inches for writing review questions, 5 inches for my main note taking area, and a 1 inch gutter on the right for random crap, like "I need more ink". The bottom row is the last two inches of the paper and the entire width, I write a summary of my notes here. I print these pages up at home on decent paper - I write with a fountain pen and I like an extra fine nib, so I want to be sure my pen won't bleed. It's not 60 lb. Levenger paper, but it's better than copier paper.

Each paper, lecture, or seminar gets a 1 page sheet of notes, even if I don't fill it up completely. Longer papers and review articles, I let myself use a couple, but I haven't been to a seminar or lecture yet that requires more than 1 page of notes.

I put as much metadata as I can think up in the top margin. The entire reference information of a book or journal article. Name of a lecturer, and biosketch notes. Date & Location. That kind of stuff.
Notes go in the big 8"x5" box (and I write tiny!) I try not to reguritate powerpoint slides, but to write consisely about what is presented. Frequently I write specific information I want to remember: statistics, biochemical pathways, references.
Stuff like "what does Smad stand for" goes in the right gutter, along with doodles, comments on my need of a beer, and theraputic swearing.
After a lecture, sometimes a day, but I try to do it while my memory is fresh, I summarize into the bottom box. If they're notes for a class, I write review questions in the left column. Otherwise, I write research questions in it during a talk - it lets me save my ideas out to one side from my notes.

If the notes are for a class, they're filed by class - this means all the information for studying is under one file. If they're notes on a seminar or paper, they're filed by topic. And by this, I mean they're filed by where they fit into my world. It's broader than specific projects. I suppose you could say they're filed by area of research. When I get enough, I give the area of research subtopics. Because the complete reference to any paper is in the metadata of the notes, I can access it easily, and associate a paper with an area of research that might not be an obvious choice. And because it's just 1 sheet, if it's really, really pertinent to another area of research, I can make a copy of it and file it under 2 different topics. Kind of an analog version of tagging.

My notes are good enough that I get a good overview of what the paper/lecture was about, what was done, what general results were observed. But for any writing exercise, you have to pull up the actual paper, it's just a fact of existence. You'll need it to double check facts/results, and to look through the bibliography for more papers to read.

If and when I get richer, these notes will probably be transferred from file folders to Levenger Circa notebooks.

I also, and I consider this very important, I keep 2 lab method books in addition to my lab notebook. My methods book and lab notebook belong to the lab, I cannot take them when I leave. But I don't want to leave my methods behind, so I keep a second, personal, methods book in a regular sized gridded Moleskine. This requires more work, because I need to keep them synced, but my personal methods book allows me to track the progress I make in refining a new bench technique, while the methods book that will remain in the lab will recieve the fully refined technique, fleshed out and written as legibly as I can. Future members of the lab will look up methods from this book - asking them to interpret my chicken scratching as I work up an immunoprecipitation method is a hard lot.

Moleskine's are ideal as method books, in my opinion, because the water resistant covers and elastic bands makes them slightly more damage resistant than the normal soft bendy posterboard variety.

I also keep a separate Endnote library for the downloaded PDFs of kit protocols - I don't need this stuff cluttering up my main bibliography.

I keep extensive paper files too, but these are generally data sheets for things I purchase, printed protocols, takeout menus, vendor quotes, etc.

I hope I answered your questions, but if there's anything you want me to elaborate on, just ask.