Update: As of Ubuntu 11.04 Canonical has switched to using light blue icons for notifications. So, I can officially say "I told you so" :)
One thing that has bugged me since Canonical launched their Indicator Applet work was their chosen colour system. I'll explain...
Certain colours can imply certain meanings. For example Green normally means "Go ahead" or "Everything is OK". Red can mean "Stop" or "Danger" or "Something's gone horribly wrong". Blue is normally associated with just "Information", especially when it comes to road signs. A quick Google Image search for "information sign" shows a definite Blue trend.
Yet, the application indicators, and specifically the message indicator, love using Green and Red. Green is used for "New Messages" but Red is used for "Your Volume is Muted" or "You Need to Restart Your Computer".
I don't know about you, but those colours don't seem to match what is basically "information" to me. In fact, both colours convey an unnecessary sense of urgency.
So, to make things a bit more mellow, I've created Blue versions of the above icons. I find them much nicer. To install just copy the "apps" and "status" folders over the ones in /usr/share/icons/ubuntu-mono-dark/ . If you decide you don't want them any more just reinstall the ubuntu-mono icon theme.