does any one know how to make the icons for t-zones and IM and other downloaded applications transparent?

You cannot alter third party icons.

even if you use different icons for the 3rd party apps?

Nope, the applications don't show up in Theme builder, so you can't alter them.

you can, however hide the icons.

---
If you figure out how to use different icons for the 3rd party apps, let us know. That's the problem, you can't use different icons for 3rd party apps, only the ones included in the app.

Hope this helps.
Rcbjr.