Not sure how this works in windows, but I’m pretty sure what I’m going to suggest does already exist there.
When sametime contacts are opened in a new window, tie the window to the systray icon like every other im app on the planet, please. This would be such a nice change. I guess the only real win here would be the ability to minimize it to the tray, but IMHO that is a big win. As of right now there is almost no point in having the systray icon (yes, I realize it offers state change).
Subject: Agreed that there is a lot more we coudl do with the system tray and Embedded Sametime
Hi,I agree that the system try with the current embedded Sametime gives hardly any benefit, and at Lotusphere 2008 I gave a presentation where I asked for for feedback on several different ideas of what are the most useful things to do.
Unfortunately, we were not able to deliver these ideas in Notes 8.5. They are on the list for the next possible release.
Subject: good enough for me
didn’t expect it between beta and final anyways 
keep up the progress and good work.
Subject: Loss of functionality.
Mary-Beth,
If it helps to prioritize, updating the system tray icon to bring focus to the contact list on click would restore functionality lost in moving to the integrated client for those upgrading from the standalone ST clients.
Thanks,