In general order of most scans, which websites have scans of Apple 2 documentation and magazines? I've done some searching and found various websites.
For example, http://www.apple-iigs.info/ has a lot of scans.
After listening to the Open Apple podcast, I think it would be helpful to have a definitive place (ie here) with a list of websites with Apple 2 scans.
Here's a list - feel free to edit this answer.


http://www.apple-iigs.info/ - huge amount of magazine, software and documentation
http://apple2scans.net/ - mostly technical manuals
http://www.whatisthe2gs.apple2.org.za/ - box scan of Apple IIGS software
http://www.macgui.com/kb/cat/4 - big range of pdf scans - game manuals, technical, etc
http://members.iinet.net.au/~kalandi/apple/aug.html - Sydney Apple User Group newsletter
http://juiced.gs/samples/ - some free issues
http://apple2history.org/downloads/ - Apple II and AppleSoft red and blue book
http://mirrors.apple2.org.za/Apple%20II%20Documentation%20Project/ - Manuals for computers, peripherals and software