For your Skype group, experiment with a seriously old-school device: the caller.
For the whippersnappers, the caller was a feature of 1st edition D&D. The caller is "kind of" the party leader - though nobody has to follow his or her orders. Rather, the caller serves as the organizer of the player side of the table - almost an assistant DM in charge of keeping the party manageable.
Pick one player to be the caller each time. (Shy players can be left out of the rotation if they don't want to stretch themselves.) It's the caller's job to solicit input from each player in turn, to be the principal voice of the party's official actions, and to coordinate any off-table discussion.
With Skype and Maptools, have players who want to speak use the chat window. Use the chat window ONLY for this, so that it doesn't get confusing. Players can just put up a "!" symbol when they have something that needs to be said. They can use "!!" or "!!!" to indicate urgency. The caller can then recognize people - "OK Phil, go ahead." Then when Phil is done, and Alex and Alice have "!"ed in, "OK, Alex, your turn."
The key to making it work is a little bit of discipline from the players. They have to shut up, in other words, unless they have something material to add. As the DM you can win their eager cooperation by giving small XP awards for players who are good at modulating their behavior, and perhaps giving a useful magical trinket (1x/day get a +2 on a roll, or something similar) to the player who does the best job each session of respecting other players' input.
Edited to add: as DM, once discussion has taken place, use the caller as your go-to player for asking "so what did you finally decide to do". If players are just absolutely opposed, they can act individually, but let people know that the expectation is the caller will make the final summary decision for the group and assess the weight of opinion. Talk more to the caller, less to the other players.
This is the one- we'll certainly try this. I suggested something like this to the players last night (actually around about 2 AM), one player leads each such encounter/interaction.
Excellent.
Anyone have any other suggestions- particularly for how to enable the players to keep a track of the questions they've asked and the answers they've recieved- that can be viewed by all players in real-time?
Cheers goonalan