I believe that the iPad is going to be our number one research and note taking tool, so that is why I have made a page dedicated to just note taking.

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Notability ($4.19 for iPad; $4.19 for iPhone/iPod Touch) Import PDF files, screen captures of websites, and photos and then use Pen, Highlighter, Text and rubber tools to annotate. Handwrite your notes, draw diagrams, use the shapes to create diagrams.

Inkflow (Free for iPad; Free for iPhone/iPod Touch) Inkflow Plus ($10.99 for iPad; $10.99 for iPhone/iPod Touch) The free version has only one colour (black). The paid version has several colours. This is more of a notetaking app but it is great for Sketchnotes
Penultimate ($1.29 for iPad) Write (by hand) notes, draw pictures, annotate photos. Create notebooks of your writing or notes.
Voice Dictation ($1.29 for iPhone/iPod Touch; $1.29 for iPad) Record your voice and change it into text
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Pages ($13.99 for iPhone; $13.99for iPad) Presentation making software. This is a cutdown version of Keynote available for Mac in the iWorks package
Note Taker ($6.59 for iPad) Hand write your notes. This app will shrink your notes so that they are able to be read easily. Would be a great publishing tool. You can annotate over PDFs
Noteshelf ($8.29 for iPad) Notetaking app with several templates and colours. Very smooth to use, would be a great presenting tool for students for publishing
Tapose ($9.99 for iPad) Comprehensive Notetaking app, allows handwriting, drawing, typing, sticky notes, highlighting,
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Soundnote ($4.19 for iPhone/iPod Touch; $4.19 for iPad) Take notes, make drawings, take photos