I have been trying to figure this out myself for about a year. I'm a graduate student, just finished my master's thesis and working on my PhD. I hate taking notes in Word because you have to constantly open and close pages. Looking for something that kept everything in one place I tried DevonThink, Yojimbo, KIT, Journler, Mori, OminiOutliner Pro, MacJournal, and Notae. The three that have stuck around are Journler, Yojimbo and DevonThink Pro.

I use Journler daily and for all my notes because of the integration with iLife and the ability to keep ppts, email, pdfs and any other file linked in right with my notes. I'm not a fan of the deleting/organization of it all th time- the numbers next to it get confusing and I wish you could view all the subfolders and items inside each root folder like you can in DevonThink but the interface is nice. You can also record audio and video right into the application as well as photos. Did I mention Journler is FREE!!- hard to believe especially for what it does

I use Yojimbo to keep track of sites I come across primarliy that I want to come back to. I find that I store a bunch but don't go back and retreive it out of Yojimbo often (but I know it is there when I do want it)

DevonThink I'm slowly getting into it with my personal life- managing receipts, medical records, travel information including passport records, frequent flyer numbers, etc.) I want to use it for EVERYTHING (writing papers, taking notes, organizing PDFs, but not there yet- it doesn't support excel or ppt docs which I like about Journler because my profs post the ppts from their lectures which I can insert right in with my notes from class.

Side note- I won't go back to Schoolhouse until I can integrate with iCal- previous version had this but he took it out, not sure why- integrate ical to do list into the iphone (still mad and confused why it isn't there) and my life for school purposes is GREAT!