I do most of my installs from source and I use stow to manage my packages.
http://directory.fsf.org/GNU/stow.html
As a convention I install all software in:
/usr/local/stow/package-<version>
There are many advantages to using stow here are a few.
You can have many versions of a single software package ready to install.
If something goes wrong its easy to roll back.
Its easy to uninstall packages.
Its easy to transport your stow dir to a new system and install all the packages.
Here are the basic steps for installing say ... net-snmp?
install stow
mkdir /usr/local/stow
get net-snmp-5.1.2 (this is just an example any package will do)
mkdir /usr/local/stow/net-snmp-5.1.2
unpack net-snmp
./configure --prefix=/usr/local/stow/net-snmp-5.1.2
make
make install
cd /usr/local/stow
stow net-snmp-5.1.2
DONE