I know that this isn't exactly what you asked for, but iptables in linux supports bandwidth throttling (I believe that it's called "traffic shaping"). This could allow you to stop one user taking over all of the bandwidth for other users.

For http downloads, you could also try setting up a proxy server using apache (or squid - but I am less familiar with it than apache). The mod_bandwidth module for apache will allow you to control how much bandwidth people on different machines can use. This would also allow commonly accessed files to be cached on the proxy server.

I don't know if any of the perl tools will allow you to control the bandwidth that they will use - although if you're planning to write a system to schedule downloads for outside of office hours, you may find that you just don't care, as no-one else will be using the link at this time anyway!

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