FTP sites:

ftp://ftp.info.apple.com/Apple.Support.Area/Apple.Software.Updates/US/Apple_II/
Apple Computer FTP site (System Software, HyperCard GS)

ftp://ftp.apple.asimov.net/pub/apple_II
Asimov FTP site (Lots of disk images of older programs, semi-legal pirate site.  --- please use this one only if you can't buy your favorite program anymore !

http://babylon.caltech.edu/a2archive.html
Caltech FTP site (Second largest Apple II archive)

ftp://ghostwheel.ausom.net.au/pub
Ghostwheel FTP site (Darn slow site, good selection, FTP access preferred)

ftp://ftp.gmd.de/if-archive/infocom/interpreters/appleII/
GMD institute (Infocom stuff)

ftp://ground.isca.uiowa.edu/apple2
Ground FTP site (Premier Apple II site - tons of PD!)

ftp://207.170.28.12/pub
Montipora FTP site (Mirrors many sites)

http://spacelink.msfc.nasa.gov/Instructional.Materials/Software/Apple.IINASA FTP site (Space-related stuff)

ftp://ftp.stolaf.edu/pub/apple2/
St. Olaf college (Misc. stuff, not much there)

ftp://ftp.ms.uky.edu/pub/appleII/
University of Kentucky (Mostly older stuff)

http://www.umich.edu/~archive/apple2/
University of Michigan (Another older site, WWW access preferred)

ftp://ftp.cc.utexas.edu/gifstuff/apple/
University of Texas (A few older GIF programs)

ftp://ftp.uni-kl.de/pub0/apple2
Universitaet Kaiserslautern (Various PD)

ftp://wuarchive.wustl.edu/systems/apple2
Washington University (Mostly older stuff)