Software I use & recommend

Here list of my 'software alternatives' decisions which makes my Gentoo installations more secure and reliable:

hardened-sources
I use Gentoo Hardened, this include patched kernel sources and toolchain.
runit
Runit is improved version of DJB's daemontools. It make system boot/shutdown, restarting services and log rotation really reliable.
socklog
Socklog replaces usual syslog and klog by simple and reliable alternative.
djbdns
Djbdns is reliable and secure alternative for bind.
qmail
Qmail is reliable and secure alternative for sendmail (actually I'm using netqmail). Probably postfix is also acceptable alternative, but I've no experience with it.
qmail-pop3sd
qmail-pop3d used with sslserver (from ucspi-ssl) turn into secure POP3 service (Maildir only).
3proxy
3proxy is good alternative for bloated squid.
twoftpd
twoftpd is simple, secure and efficient FTP server. Sadly, I've some issues with it, but can't find better alternative yet.
dcron
Dcron is lightweight and minimalistic cron daemon.
fastcgi
FastCGI (in external server mode) is much more portable, secure and manageable way to efficiently run CGI/PHP scripts - unlike SuExec, mod_perl and mod_php.
asciidoc
AsciiDoc simple yet powerful documentation system.

Also: Vim, Mutt, Pidgin, Opera, Clementine, FluxBox, Conky, rTorrent.