for the security bugs of which I'm aware (I'm not a JA player) the examples which come in my mind are:
- fix for q3infoboom bug:
http://aluigi.org/patches/jaw101q3infofix.zip- fix for jamsgbof bug:
http://aluigi.org/patches/jamsgfix.txt- fix for q3cbufexec bug:
http://aluigi.org/patches/q3cbufexecfix.lpatch- fix for directory traversal:
http://aluigi.org/patches/q3dirtravfix.zip- disable the rcon half-second limit:
http://aluigi.org/patches/q3rconz.lpatchnote that the above are mainly referred to the Windows server, although except some of them the other work also with the Linux server