One of the issues I've noticed that could be tricky is whispering. You have to type it in each time and to each player. Notes and what not go to everyone by default.
I would like an easy button of sorts where you could jump to a separate window with whichever players you wish to speak with.
An example in play would be if I'm running a game with insanity or say illusion magic. Someone opens up a door and encounters an old woman. Everyone sees the old woman but the single player who sees monster.
Now the player who sees the monster pulls out a weapon and starts shouting for everyone to stay away. The other players go "he's lost it" while he thinks "clearly this monster has everyone under it's spell."
To keep everyone in character and keep a solid in character narrative going (where players actually see what their character sees) it would be made easier by being able to make GM only windows to each player or group of players to send them material.
This could also be useful for psychic players (They catch an image you send to just them). Or separating players dramatically without disrupting the flow of the game, by just dropping a player or two into a new window, cutting them off from the group.
In particular there are a number of games that would benefit from this.
Call of Cthulhu, World of Darkness and any game where psychics or illusionary magic plays a big part.
If is done there should be the option of a single secret window (where you can communicate incognito to one or more players) or a separate window that removes players entirely from the main screen.
I could envision a drop and drag method for removable of players onscreen, which in that case would place their webcam on the second screen unable to see you until you switch to their window.
While a [Start separate window] option could be clicked opening up a second screen with just the players you want for the purposes of sending images, video, notes or chatting, but the webcam wouldn't be used here to prevent other players from noticing the conversation you are having with the separate players.