I have the same type of issue with the operator channel. With numerous operators (we have roughly 18) logged in there is the possibility for lots of traffic in this channel. We need the operators to be able to see what's said here, but not all of them want to see pop-ups for everything that happens in the operator channel.
As an example, sometimes we have what I'd call watercooler chat going on in there and not all our operators care to see Pink Floyd trivia popping up in their systray every 3 seconds - for those operators this is extremely annoying. The ability to filter which channels cause popups would be perfect.
We'd also like to be able to filter these by department so support staff aren't bothered by sales requests.