Another PhD student here.

My flow is very similar to bluloo, and I, like many others, have purchased more tools than I currently use. It's embarrassing, frankly. I suppose I'm doing my part to support independent Mac software.

One problem with too many choices, however, is that I frequently found myself trying to decide which tool was the absolute perfect one for the job. It slowed me down -- expecially when I second-guessed myself and switched horses mid-stream. Very unproductive.

My current system has been pared down to be exactly what I need and nothing more.

1. VoodooPad. I take all my notes in VoodooPad. I write drafts of papers (in smallish snippets) in VoodooPad. I draft important emails to my advisor in VoodooPad. If I'm going to write something down on my computer, chances are it will start in VoodooPad.

With VoodooPad, I've chosen to delete a number of other tools from my machine, many of which are very good. Scrivener, Journler, Mori, Copywrite,... there's more I'm sure. In the end, each of these performed the same task for me, but each with a slightly different design philosophy. VoodooPad is the one that works best for me. While YMMV, I recommend you pick one and stick with it. Avoid being a fickle bastard and installing one of each on your machine. You'll regret the distraction.

If you feel compelled to give each one a fair shake, give yourself limits. For a project, choose one and don't allow anything to change your mind until you've completed the project. No software is perfect, and you'll never discover the joy of power-use or the surprise of dead-simple workarounds until you've forced yourself to confront the application's weakness.

2. From VoodooPad, any significant writing goes to Mellel, where it stays until it's finished. With the newest feature additions (I can now add style inside my auto-titles!), I think Mellel is amazing. I write better because I use Mellel.

I have Word installed because I was able to purchase MS Office for $60 with an awesome academic discount. I use Excel sometimes, so it's handy. I never launch Word.

3. For commenting on student papers, I use iWork's Pages.app. I can work faster in Pages, adding comments to their drafts, than I can in Word. Because Word is in desperate need of an update. Honestly, it didn't always suck, but it's been dramatically overtaken by others in the market.

Yes, I have three word processors on my machine. Four if you count TextEdit. But because I have clear lines of when to use each, it's not a problem. I write scholarly papers in Mellel, end of story.

4. All references are stored in Bookends. Sometimes I'll grab references using Zotero (Firefox extension: look it up) and then import them into Bookends. I heart Bookends. It's not as pretty as Sente, but I've adapted to Bookends' quirkiness.

5. Of course, all PDFs, while linked to their reference in Bookends, are also indexed by DEVONthink. Because doing serious academic work without DEVONthink is like trying to read a book by candlelight. Sure, you could do it, but why not use the superior technology of a light bulb? I'm not kidding when I say that scholarship without DEVONthink is almost unthinkable.

6. I have Adobe Acrobat Pro installed just so I can easily OCR any PDFs that need it.

7. Pzizz, because with this I don't nap and if I don't nap I tend to overwork and get sick and fall behind and my life sucks. Pzizz (along with my nike+ipod setup) keeps me out of the doctor's office.

Virtually everything else is web based. I use everything google for my mail, calendar, rss reader. And so the only other thing I use is iTunes, I guess. Well, there's Adium, which isn't really scholarly and doesn't need to be mentioned. And TextMate, but that's not for my scholarship, either.

Again, my best advice for using technology for your PhD is to avoid smogasbordism: pick one for each category and let all the other (unquestionably worthy and well-written) applications alone.