I used to work at a large public university. One day, a grad student brought me his laptop and asked if I would take a look at it because "the Internet [was] really slow." It turned out that his computer was part of a botnet controlled via IRC, and it was being used to attack hosts on the Intertubes.
After sniffing the IP address + port of the IRC server and the channel name and password the botnet was using, I joined the channel with a regular IRC client. "/who #channel" listed thousands of compromised clients, including hundreds with .edu hostnames. (One university had a dozen hosts from .hr.[university].edu in the channel. Sleep tight knowing your direct deposit information is in good hands.)
There was no way I could notify everyone, so I concentrated on e-mailing abuse@ the .edu domains. In my e-mails, I explained who I was and where I worked, that one of our computers had been compromised by hackers (yeah yeah terminology), and that in the course of investigating, I found that computers at their university had also been compromised by the same hackers. I also included a list of the compromised hostnames at their university and the IRC server's information so their networking people could look for other compromised hosts connected to the IRC server if they wanted to. Relatively basic IT stuff.
I didn't get replies from the majority of the universities I sent messages to, including the .hr.[university].edu one. I got a few thank yous, but I got just as many replies from IT Security Officers and CIOs (including at big name universities) accusing me of hacking their computers and demanding that I stop immediately or face legal action.
Those people just didn't understand, and they were in charge of (or ultimately responsible for) their universities' IT security efforts... It was completely mind-boggling to me at the time.