Tools
PuTTY
Encrypted SSH client for Windows http://www.chiark.greenend.org.uk/~sgtatham/putty/
OpenSSH
SSH server and client software for multiple platforms http://www.openssh.org
OpenSSL
Open-source SSL library and tools http://www.openssl.org
PGP File, Email, Disk and Network encryption http://www.pgp.com
GnuPG
GNU Privacy Guard (PGP compatible) http://www.gnupg.org
OpenPGP compatible products
Software (commercial and otherwise) which is compatible with the OpenPGP standard
http://www.openpgp.org/members/
eTrust Access Control
Host-based IDS/IPS, rootkit detection/prevention and more (formerly named SeOS) http://www3.ca.com/Solutions/Product.asp?ID=154
LIDS
Linux Intrusion Detection System.  Host-based IDS/IPS, rootkit detection/prevention and more http://www.lids.org/
TCP Wrappers Limit incoming  connections to server ports ftp://ftp.porcupine.org/pub/security/index.html#software
TripWire Detect unauthorised file changes http://www.tripwire.com
OpenCA
Open-source CA software http://www.openca.org

more coming...
CERT Tools Page
CERT's list of security tool resources
http://www.cert.org/other_sources/tool_sources.html