There's an interesting piece of advice at the bottom of this post - the author symlinks /bin, /sbin, and /lib to /usr/whatever. Anybody else have an opinion on that practice? It's kind of unnecessary, but it also doesn't break anything.
There are a variety of tools that live in /bin but are symlinked in /usr/bin, at least on my 10.04 LTS box:
$ for f in /bin/*; do [ -e "/usr$f" ] && echo /usr$f; done;
/usr/bin/dumpkeys
/usr/bin/ksh
/usr/bin/less
/usr/bin/lessecho
/usr/bin/lessfile
/usr/bin/lesskey
/usr/bin/lesspipe
/usr/bin/loadkeys
/usr/bin/mail
/usr/bin/nano
/usr/bin/tcsh
/usr/bin/touch
/usr/bin/which
/usr/bin/zsh
This has the potential to blow something up during the installation procedure if it is not carefully crafted to realize that these files are the same and to ignore link's failure.
Which I find is actually quite problematic; "make install" by default puts things into /usr/local, and I would prefer to distinguish between things I've installed and things ports have installed. (Specifically, I need to build my own mplayer, but I also need the ports version installed as some other ports depend on it).
Feel free to change the prefix passed to the packages you install by hand. /usr/local is the default used by almost all packages I am familiar with, if for example you want /opt you have to modify that yourself.