A few tools that are invaluable already, a few that are becoming so, and a few that I think will in the future. This is the junk (Anyone watch that Extreme Makeover: Home Edition show?). Some are more well-known than others.
meld: graphical diff/merge
wiggle: applying patches with conflicting changes
quilt: patch manager
herdstat: Gentoo-specific querying tool for herds, developers, categories and packages
splat: Gentoo-specific portage log analyzer
esearch: Gentoo-specific caching package search. Way faster than portage.
cpu: CLI LDAP user management. May try switching to diradm soon, since its by one of our Gentoo devs, robbat2.
logrotate: keep log size manageable
sudo: selectively let people run commands as root
superadduser: for people who don’t like reading the useradd man page
nano: a surprisingly featureful editor
screen: detach running sessions
detox: cut weird characters out of filenames
strace: useful in debugging
ccache: speed up repeated compilations
keychain: SSH agent manager — don’t type the password every time