There is a standard for this, It's called the FHS that stands for Filesystem Hierarchy standard
However, I can give you the basics.
/etc is where most systemwide configuration files go
/proc is a funny directory... it's actually a virtual directory... you don't want to mess there (probably can't as user).
/home is where the home direcotries of the users are stored.
/root is the home directory of root
/usr is where most user programs go (like OpenOffice). There are also libraries here and man pages too.
/dev is a virtual direcotry that points to hardware (don't know much abut this one)
Normally programs are installed in /usr (systemwide) or in the user's home directory (for single user).
/bin and /sbin contain binary (executable) files, /sbin is a directory that only root can execute... it has admin binaries (like ifconfig, drakconf/linuxconf/whatever, etc)
/var has the logs and spool of the system (also the sendmail storage).
Ok, here is how I organize my FS: /home/alan is where I have EVERYTHING. downloaded software (rpm, tgz, tar.bz2) goes in /home/alan/downloads, documentation (man pages, pdf books, html tgz, etc) go in /home/alan/download/documentacion. I use the default direcotry for installs (/usr). I try to stick to the FSH as much as I can...
from the FHS TOC
3.4 /bin : Essential user command binaries (for use by all users)
3.5 /boot : Static files of the boot loader
3.6 /dev : Device files
3.7 /etc : Host-specific system configuration
3.8 /home : User home directories (optional)
3.9 /lib : Essential shared libraries and kernel modules
3.10 /lib<qual> : Alternate format essential shared libraries (optional)
3.11 /mnt : Mount point for a temporarily mounted filesystem
3.12 /opt : Add-on application software packages
3.13 /root : Home directory for the root user (optional)
3.14 /sbin : System binaries
3.15 /tmp : Temporary files
give it a look... it's interesting reading...