OK Found it! Messaging menu actually uses alphabetical order.So chat comes before evolution or gwibber. So the order is for various applications which use messaging menu is like this:
So when using pidgin, the file-name (under /usr/share/indicators/messages/applications) has to be changed to "chat" from "pidgin".
But the file content remains the same which is
Also the name section of the desktop file (in above case pidgin.desktop)has to be changed to "chat" from "pidgin".
Finally one needs to recompile messaging menu replacing "emapthy.desktop" with "pidgin.desktop" inside default-application.c
file located under /src directory of the source package( indicator-messages-$version/src).
Same with Evolution/Thunderbird.