All the below, assumes you are using a standard Debian style networking setup: ie no network manager or wicd. If you are using these sort of tools, the standard Debian tools will probably not work and you should either use your network manager or wicd frontend or, as suggested by ms3fgx, use a low level tool like ifconfig.
Can you please post you /etc/network/interfaces file and the output of
just before and after calling "/etc/init.d/networking stop".
Also, if you just want to bring down a specific interface (eg eth0) on a system using a Debian style networking setup, you can bring that interface down with:
This will ensure that any hooks defined for that interface will be run.