I'm a grad student in the humanities, so most of my scanning is out of books, so I use the OptiBook 3600 under VMWare Fusion (long live continuity view). It's reasonably quick (only marginally slower than a copy machine), scans all the way to the edge of even this thickest text, and output is exactly what I need. I save the images as TIFFS where I can get to them from my real OS (X). When I do have loose papers to scan, I have an HP 3015 laser multifunction with a sheet-fed scanner (it has served me well under Windows, then Linux, and now OS X). I've not found it convenient to scan in my note cards—I probably won't be able to read them later anyway, so I just do the capture by keyboard every day (or so, really).

I use Acrobat Pro to wrangle my scanned images. I've found the output the best and the file sizes (when the settings are right) quite acceptable. I have about 7GB of scanned documents, so this is a concern to me. With my university's site license, the cost is not really an issue, so your situation may vary. I then use Yep for tagging/visual discovery, although most of my launching comes via Quicksilver or Bookends. Consistent file naming is the key. Given my purposes, "Author_Short title" is my preferred method, making it easy to find what I need from whatever app I'm in. I've also found that a single directory for all of the research works the best. (Personal/administrative scanned items also have a single directory, as do student assignments, etc.)

I typically do my reading in Acrobat (unless it's just a quick glance, then I just use the loupe tool in Yep or Preview), using a mix of highlighting and the occasional sticky note, but for the most part I just take notes in a text document using the 'append to file command' in Quicksilver. I've found the best way to read is to stick my widescreen monitor in landscape, so that I'm basically staring at a large sheet of text in front of me. I then clean up the comments, do a save as, and add it to the appropriate Smultron project (tabbed text editor).

I'm about two-thirds of the way through an almost paper-free review of all the literature on my topic. I do print my notes while writing sometimes, but other than that, it's just drafts for other people. It's a different kind of workflow, but that's what works for my circumstances.