like everyone else said, the package manager will put things where it needs them to be put.
I tend to have a projects/ folder where I checkout my random git projects.
Eclipse likes to keep its projects in workspace/ Depending on how much development I do under eclipse I would do something like $HOME/workspaces/{AndroidStuff, CrazyRandomIdeas} depending on if the things I'm working on should be in its own workspace or is a small project.
Also, occasionally I like to install things in my $HOME since i'm just playing with things and don't want to pollute my filesystem, which I tend to put in $HOME/local. Again this is just my style.. but I end up with
$HOME/
bin/ -->symlinks to binaries I installed locally and added to $PATH
local/ --> local installs of applications, libs etc.
projects/ --> git check/svn checkouts etc of random code.
workspace/ --> eclipse stuff.
Try not to install anything in your root filesystem (/) unless you package it. It's a royal pain to uninstall things, (there's always a make install but rarely do you ever get a make uninstall). Also, that's the entire point of a packaging system, to keep track of your programs, files, configs, etc.