Ok, I'm definitely not all "implemented"... but here's what I've started and it's already been helping!

First, I run Kinkless kGTD. I can set that up with various projects and subprojects... [i.e., those 5 major projects your thesis is revolving around, and the 20+ subprojects which support those 5 that all have major numbers of tasks to complete...] I try and keep these to tasks only, and ideas for brain-storming in the future. Kinkless allows me to put references to folders of files etc., into the system as well, so I can simply click on a folder icon to bring up the files which may be required for my work in that area quite easily. It syncs to iCal, so iPod integration etc., is possible, but I'm finding I'm not using that as much.

What I have been doing as of late, is keeping a Moleskine cahier, with a rubber-band around it, and about 5-8 index cards slipped inside. The cahier leaves me space to brain-storm on the fly, have those middle of the hall-way discussions with the supporting scientists around the university, and keep my notes together. I print my iCal calendar out for 2 weeks onto an index card (3x5) by first printing it at 5x7 and scaling down to 3x5 in preview (fairly simple). I bought a small iP1600 from Bestbuy the other day ($50) for printing the cards needed.

I also print out the kinkless task/project cards for when I'm away from the computer. So far the calendar has been critical, as well as a blank index card with running dates for an on-the-go inbox.

For journal articles, I have to plug a fantasic program on the mac- BibDesk. Completely free and constantly being updated. Excellently stable at this time. Since I write in LaTeX, I need a bibtex database for my journal articles anyways. BibDesk also organizes my articles by first-author quite nicely, and is easily searched as well. [Not to mention it auto-completes in many programs- with latex and bibdesk and iTeXMac, everything just works. Couple that with mac's Preview and cropping /saving out of journal articles critical graphs etc. and you now have a powerful system for writing your thesis!!]

For my e-mail, I have thunderbird working through Yamb and Growl notifications. So, if an e-mail comes in, and it's not time-critical, I can simply ignore it without even having to bring my e-mail app forward. If it's time critical and a short item, I can go do it, or slip it into my inbox to complete. I also have a @action folder in my inbox that gets run through every couple days to ensure I'm doing items needed to be done which are e-mail related but may not be critical enough to be in my kGTD inbox. For the first time, my inbox is actually fairly blank, and items get dealt with and filed away based on the 2minute rule. :) As long as it's work-centric at the time, this should be helpful not hurtful.

Finally, I'm also attempting to file better on the computer... things for work go in the major work directory, then get filed in appropriate sub-directories. If there's something I'm working on, I bring an alias to the desktop, but nothing sits in 'nowhere' folders which aren't filed anymore. [At least in principle. ;)]

Oh! A bit more about the bibliography app and filing... when I search on say ISI knowledge web, or on Engineeringvillage.org... the output can be imported directly into BibDesk, and from there, a simple drag and drop into Bibdesk shuffles off the journal article under the first-author name. :) Very seamless.

My office at the moment needs serious help, however, as I have not yet implemented everything here. I do have a label-maker and have used it numerous times to organize items, but it's just not complete yet. Things are under the gun for me now, and I can't devote time to it, as I'm already 6 months behind on a project (yikes, eh? well, the research world can be like that sometimes... :(... ) it doesn't do well for the brain, however, to know you have these things hanging over your head, and that's where kinkless helps. It eases up on that pressure, as you know where to look for those items that can't be lost. :)

Ok, I've typed too much, I better get back to work. I wish you the best of luck with your Thesis!! I hope I can get through this year as well. :?

[Also- wanted to mention- rsync for the mac thesis-writers out there... I'm working on a multiple-computer backup system that on a single click will backup all critical work files... :) I'll be back to mention it when it finally works. :) It's all possible with rsync in Tiger... or RsyncX with lower X mac systems.] Now, go back up that Thesis!!

-Allen