Bandwidth limitations of network loopback device

You could use

acl aclname rep_mime_type mime-type

to block certain mime-types from downloading (eg iso's)

and

reply_body_max_size

to set a ceiling on the biggest files that can be downloaded

you could also use free-sa to analyze your logs to see where the bandwidth is going

http://free-sa.sourceforge.net/

EDIT: Actually squid delay pools will do EXACTLY what you need.

read this article: http://www.howtoforge.com/squid-delay-pools-bandwidth-management

What kind of routers are you using? It sounds like you're just using SOHO type routers? You might want to look at getting better routers and switches with management built in and monitorable through SNMP.

That said I'd also put in a proxy server that can log activity and block certain traffic. Proxying can help some of your speed woes, blocking can limit others.

Upgraded routers can also handle traffic shaping and limiting, as well as QoS. If you must do it on the "cheap", you could start using a Linux box (there are several turnkey solutions) to do the traffic monitoring and shaping. Install, configure, set it as the gateway for everyone's system to route through. An inexpensive box can also do the proxying work for you, and you could have options for VPN access.

We ran a SquidGuard box for awhile to filter and proxy traffic. Turned out it was also pretty good at helping track down certain malware on the network when we filtered for certain broadcasts that were scattering through the routing tables from a particular (infected) client. It was also great for getting browsing activity reports.

Just make sure any filtering or whatnot is allowed in your policies and employees are made aware of network monitoring. Sometimes it's the law, other times it's just a nice courtesy to your users to be reminded they're using company resources, not personal resources.