Here how it looks like for me with windowmaker:

==Tabs disabled==
1) First incoming message without opened chat dialogs-->dialog opened in background, message counter+1
windowmaker: dialog opened in front and with focus to the input field, because it has focus, there is no mesage counter in the title bar (actually that is fine for me)


2) clicking on Dock icon-->chat dialog in front with main Coccinella window behind it, *no* focus on the text input field, *no* reset of message counter in Dock (only in window title!).
clicking on a minimized chat window icon in the dock brings up the window, with focus always to the input field, no matter whether it was at the subject or somewhere else, the message counter in the title bar is resetted. I see how many new message are there, because the old messages are lighter gey instead of black. (actually that is also fine for me)

3) clicking on main window when chat dialog is in front-->Dock message counter is reset (note: if the chat dialog is closed first, the Dock counter is not reset)
clicking on the main window when the chat dialog is in front of it (but without focus because a different app had focus), just brings the main window to front for me, the message counter stays in the title line. Only when I click the message window to get the focus to it, then the message counter in the title bar is resetted. (that is again find for me)

4) Second incoming message-->chat dialog raised to top, without focus (bad: it should stay in the background)
I have the same here, I found the following code to be the culprit:
        # 12th June 2009 - Mirko Graziani, <email address hidden>
        # https://bugs.launchpad.net/coccinella/+bug/297580
        # Bring the window over the others, but since
        # the "wm focusmodel" is set to 'passive',
        # the user is not interrupted in his work.
        wm focusmodel $dlgstate(w) passive
        wm attributes $dlgstate(w) -topmost 1
        wm attributes $dlgstate(w) -topmost 0

What I have seen on KDE (which I find is acutally very annoying:)
Whenever I receive a message, the window shows up and immediately goes back into the background, so I have a flicker for a fraction of a second (which could cause epileptic seizures, as written in bug #297580 ;)
Because the request of raising/lowering the window was only for windows, would it be feasible to only use that piece of code on windows OS? Or would it be feasible to add sth. to the preferences interface, where the user can choose whether he wants to have those flashing or not, regardless of the OS? But then, what to make the default value of that preference?
When I comment out the line:
wm attributes $dlgstate(w) -topmost 1
Then the window stays in background when the second message is received, which would be the best for me...
However, I still wonder why it goes to background with topmost 0 on KDE but stays on top with Windowmaker....

==Tabs enabled==
1) First incoming message without opened chat dialogs-->same behaviour as without tabs
same as described above, so fine for me
2) clicking on Dock icon-->chat dialog in front with main Coccinella window behind it, *no* focus on the tab which has the oldest new messages text, *no* focus on the input field, *no* reset of message counter in Dock, message counter in the window title is reset for *all* contacts that had send you new messages.
more or less the same as above, here are the details:
generally, the last opened tab before closing the window is remembered, and opened when opening the chat window again.
When the tab that received messages was active when restoring the window, the message counter in the title is resetted
When the tab that received message was not active when restoring the window, then I see the message counter on top of the tab, and when clicking on it, then the counter is resetted 

3) clicking on main window when chat dialog is in front-->Dock message counter is reset (note: if the chat dialog is closed, the counter is also reset, so this is better behaviour as without tabs)
As I do not have a counter in the dock at all, I cannot verify

4) Second incoming message-->same behaviour as without tabs
same here