I'm sure some others on this forum will repeat me.....

DEVONthink

Or even, DEVONnote

Ultimately, it is up to you and your personal preferences.

I am using DEVONthink Pro Office and love it.

That doesn't mean a more economical solution wouldn't work for you though.

I have no experience on the matter, but I know at my uni, there is a pretty sweet student price for Endnote.
Grieser

When I bought my Macbook I did the exact same thing. After reviewing a lot of software, my school work goes through:

Omnioutliner Pro: Not just for kGTD. You will be able to buy the upgrade since Macbooks already come with the standard version. Once I got omnioutliner to open up with a freshly prepared document ready for my exact notetaking preferences, it was just like butter. Helped me a lot last year.

iWork or Neooffice: Stay away from Microsoft Office. I think it runs like CRAP, and it's just down-right wrong to pollute your mac-goodness with the likes of it. (I can't believe I turned into an actual Mac-Fanboy). iWork works wonderfully if you can afford it. I love working with Pages and Keynote. Neooffice (still in beta), is a lovely alternative - it just doesn't have the beauty of iWork.

I am still looking around for programs to help with research. I have heard of Endnote, but I know there are ALOT of alternatives. Someone else should know more.

Kind regards,
Jonathan Cisco

http://www.dreamingnz.com

OmniOutliner
Mori
Bibdesk for references (or Sente or Bookends; I'd avoid Endnote)
DevonThinkPro
Tinderbox (expensive but supposed to be the Photoshop of writing)
Textmate + LaTeX for writing
Freemind (if you want to do visual mind-mapping)
Papers (looks very interesting for references and notes but is very early in development.)

...And MOST important
a good BACKUP scheme

Bookends is, I think, a better bibliography solution than Endnote. Sente is another option. Endnote is buggy and annoying, and much more expensive than these.

Thanks for the suggestions so far. I guess I should have mentioned that this is not my first Mac -- I became a born-again Mac user shortly after OS X arrived on the scene and I used to be a school-based technology coordinator that supported a 50/50 Windows/Mac environment. Fun times...

I did, in fact, pollute my recently deceased PowerBook with MS Office and said I would do whatever it takes to avoid doing that again. I use NeoOffice (even on my Windows machine at work now -- sort of a passive protest to not being allowed to have a Mac...) for word processing, and I'm using the free trial of iWork right now hoping to bide time until iWork '07 comes out.

My concern is whether I'll be able to avoid MS Word when it comes to writing my dissertation. To be sure, it isn't the best tool, but I'm sure it's pretty much the accepted standard - especially when it comes to sending drafts back and forth to my adviser. Needless to say I don't want to start writing and be switching apps and re-learning things....

You cannot forget VoodooPad. It's excellent for taking notes.

I own a lot of these types of apps (DevonThink, VoodooPad, MacJournal...) and for taking notes VoodooPad is perfect and a lot cheaper than DevonThink. If, however, you are going to be doing more than just taking notes and want to do some heavy research then DevonThink (Pro) is what you are going to need.

I heard Merlin talk about VooDoo Pad recently on MacBreak Weekly so I'll give it a look.

Any other thoughts of what I should be looking for when it comes to actually formatting and writing my dissertation? I never could get very good at formats and styles in Word, but is there a way to get around using it in academia?

Hopefully your school has some premade templates and styles for their dissertation format. Those might be in Word, LaTeX, or something else entirely. If not, you'll have to go through their style guide and work it up yourself. I'm not a Word user, but the advice I've heard from those who are would be to use styles heavily for structural elements and other formatting.

Example: a chapter title should have a "Chapter Title" style, which is defined according to the rules of your school (maybe that's bold, all caps, centered, 14pt). If you make a mistake, you update the style definition once instead of updating every title's formatting manually.

Your school probably won't care what tool you use to compose your dissertation, only that it matches their format and style. Your advisor might be more strict. Your library may want an electronic copy for archival purposes, but they'd probably want a PDF. I did my master's thesis in WordPerfect. Others used Word, LaTeX, etc. I'd expect you could use Pages, OpenOffice, or anything else that has the required level of support for graphs, tables, or equations as needed.

I like the look of DEVNONthink. From the feature comparison, I can't see a compelling reason to go with the Pro Office version over Pro for the additional $60. I like the idea that I can actually attach PDF files since I've already started to collect quite a library... I can see the scanning and character recognition feature being a bonus, but again -- will I use it enough to justify the $60 when it seems like everything is available electronically these days anyway.

On another note -- anyone have any experience with Mellel? Looks interesting...

I also like the look of Bookends. From what I'm reading, Sente can't do full endnotes and bibliographies in APA format.

Regarding LaTeX, seems like quite a learning curve. Might be worth considering down the road, though. I'll have to talk with my adviser and see what he suggests.