SpiderNet - Macintosh Online Service
Apple Support - Older Apple software downloads
Low End Mac Low End Mac - Classic Mac OS Downloads and Updates

SheepShaver is an open source PowerPC Apple Macintosh emulator. Using SheepShaver (along with the appropriate ROM image) it is possible to emulate a PowerPC Macintosh computer capable of running Mac OS 7.5.2 through 9.0.4. Builds of SheepShaver are available for Mac OS X, Windows and Linux. See also: http://sheepshaver.cebix.net/SheepShaver.

Apple security updates

Apple Support - Mac OS 9: Available Updates dead link, use archive.org - Apple Support - Mac OS 9: Available Updates.
archive.org - Apple - Mac OS 9.2.2: Document and Software
Apple Support - Multicountry directory - Dutch Mac OS 9 and lower updates dead link, use archive.org - Apple Support - Multicountry directory - Dutch Mac OS 9 and lower updates.

Apple Support - Multicountry directory for software relevant to other languages. Links for 9.2.x updates seem to be dead. Use this as a starting point to get the different language versions. Just remove the http://web.archive.org/web/20100917074207/ from the link to the .smi.bin file. Or try here instead for the updates for the US English version.

Pure Mac - Mac OS 9 Updates
Updates for Mac OS 9
OS 9 Forever.com
Macintosharcive.org's mirror of max1zzz.co.uk contains all 9.x.x updates upto 9.2.2 in several language versions.

Archived - Mac OS 9.2.2: Document and Software
OS 9.2.3 is the unofficial update to Mac OS 9.2.2. It adds 17 system menus with 180 new commands to the Finder. Most of them are disk and file utilities. This is NOT an Apple product. By Cliff Huylebroeck. Dead link, use archive.org - OS 9.2.3.

Classilla is a free, open source browser for Mac OS 9 and where possible Mac OS 8.6 built on WaMCom, a port of Mozilla to classic Macintosh system.
TenFourFox “The world's most advanced web browser. Finely tuned for PowerPC”

ixsoft
Aspyr (for Doom 3, Quake 4, NWN 2, Stubbs the Zombie among others)
Chronic Logic (for Gish and others)
RuneSoft

Server Density Blog - GoDaddy SSL Certificates and Cannot Verify Identity on Mac/Safari
Symphonious - Tomcat, OS X, Safari and GoDaddy SSL Certificates

The University of Texas at Austin - ITS - Help & Support - Importing Your Certificates Into Mac OS X Keychain
The University of Texas at Austin - ITS - Help & Support - Backing Up and/or Moving Certificates in Mac OS X

We Saw a Chicken... - When you really haven’t chosen not to trust: Citrix, Mac OS X, and Entrust certificates
archy.net - Citrix Online Plug-in for Mac, SSL Error 61: You have not chosen to trust...