Just noticed this post since the thread has sort of been revived in the last few days. In virtually any program you can print from on mac, you can convert to PDF. Just click "print" (File > Print) and in the bottom left corner where it says "PDF", click that and go to "save as PDF". Whatever attributes you have set for the printing, thats what the PDF will look like. Example: If you go to PowerPoint and click print, then change the print settings it to "6 per page", "4 per page", etc., then when you save as PDF, this is how your PDF will display. It's very convenient. Like DropShot said, some people just prefer printing and writing, but I'm quick enough using the annotate feature in Preview that I prefer to type notes that way. I forced myself to do this not only to save space, but because I still write like a 7 year old.
As for the classes where they had syllabuses ready for us, I would take handwritten notes on those. However, some classes will have digital OR hard copies of the syllabus, in which case I went for the digital versions. For Biochem and Phys in particular, a digital version of the syllabus was not often available.
A disadvantage to digital notes is you're limited on how much you can free-hand things, but with the boxes, circles and arrows available in preview, I haven't felt like I need to draw hardly anything I can't. Most of the time, all (or 98%) of the information being taught and tested over is on the ppts you're given anyway. Some people get away without taking any notes and just study it all later. Whatever works.
Whatever you do, get an external hard drive. The last thing you want is to lose all your files and have no backup.
Hope that helps!