Nothing will ever be as good as paper and pen but if you are absolutely adamant about going digital as I was, Noteshelf + my tools is the best solution I've found after spending a lot of time testing things out. Obviously I only tested what was listed below so take that with a grain of salt but I researched and went over others not mentioned.
THE TOOLS:
iPad 3, Adonit Jot Flip Stylus
THE APPS:
Noteshelf, Ghostwriter Notes, Paper (by Fifty Three), Note+
THE BREAKDOWN:
After spending weeks researching, reading, watching youtube videos, etc... I narrowed down my decision on the best note taking apps to Ghostwriter Notes and Noteshelf of over a dozen other apps. Since Paper and Note+ were both free, I downloaded them to try them out as well. Here are the results...
Note+ - Total garbage. Not even worth rating as this app would receive negative points if I could issue such a thing.
Paper - Probably great for other purposes but totally not designed for note taking in mind and thus would be rated incredibly low.
Ghostwriter Notes (paid app) - Sounded sooooo good in theory and in videos but in practice, there were so many things wrong with this app. Regular note taking was completely unresponsive unless you plan on writing in font size 80. The only way around this problem was to use the zoom in writing feature but that left very little writing space at a time and the text in the box were often pixelated and there is still some lag time. The writing guard sucks as it required constant adjustment, etc. In essence, don't bother.
Noteshelf (paid app) - This was THE best option I found. The flaws were few. And while it lacked some options (such as PDF annotation), those are unimportant in just plain note taking if that's what you're primarily interested in. It does the job incredibly well (albeit not 5 stars). This app does a good enough job that I'm sticking with it.
FINAL NOTES:
I own almost everything Apple so iPad has always been my tablet of choice (I've owned all 3 versions). Yours may differ. In terms of picking stylus, I spent a couple weeks researching this as well and going over more than half a dozen kickstarter projects (new and old) as well. Jot Flip ended up being the one I liked best. For awhile, I was debating between that and the Cregle iPen until I saw a review video on YouTube showcasing the iPen (apparently the response isn't base on the tip but a sensor on the side). I then decided Jot Flip was the way to go. I wanted a stylus that resembled a pen tip and note one of those thick rubber heads you often see which I'd imagine blows for actual writing.
As a side note, if you just want a stylus without the pen, you can buy just the Jot or Jot Pro. The difference is the Jot Flip includes an actual pen on the opposite head. I wanted to keep the pen option available and was totally not disappointed. Its a really nice pen.
I see it as more of an appliance than a tablet, serving one purpose really well. It's like an etch-a-sketch for adults. I find that in programming I often need to scratch paper to track variables or do simple state diagrams and once I've solved the problem I no longer need the paper.
I haven't tried it IRL yet, but at that price, I think I will. Call it a kindle meets etch-a-sketch.
http://www.improvelectronics.com/us/en/boogie-board-LCD-writ...
1) small size (think mine's 7 inches or so?) 2) difficult/impossible to write small enough to fit a good amount 3) no way to save pages (in any way). I tried to hack my way around this by snapping pictures of full pages, but it just became too much of a hassle.
There's this really good (currently beta) app called "Write" though. Not sure if they'll be extending its consumer base anytime soon.
https://www.youtube.com/watch?feature=player_embedded&v=...
https://play.google.com/store/apps/details?id=com.styluslabs....
its a fantastic app that works with my stylus so i'm pleased.