This article is very much opinion based and where you fall on the question will likely depend heavily on the type of game you play. For instance Skype parties are frequently used in World of Warcraft groups or for games like League of Legends.
For those of us like myself who play a roleplay-enforced game, where breaking character is considered rude and taboo, where using information gained via OOC means is frowned upon and where using information across alternative characters will get you punished by the administration, planning utilising the methods available in-character to discuss a possible coup, or organise a raid is more than encouraged. It's necessary.
This can open us up to some problems. In the top MUD that I play, Achaea from Iron Realms Entertainment, everything must be typed. Intricate, on-the-fly plots can take some time to type out, rather than just outlining it quickly by voice over a chat. For speed and input of a group conversation, the voice chat groups get the win on this front.
By discussing things in-game we also open ourselves up to spies: perhaps someone is eavesdropping at the door, or that letter is read and copied before it reaches its destination. Infiltration and spying is a very valid form of roleplay, and when done properly can be a right pain in the backside for the plotting character. So for security's sake, I suppose the check goes to the OOC chat group again.
This is all well and good, but we need to remember that we play games with other people, winning is great, but a lot of fun can be had from there being a risk involved: the chance of losing. Actually having your plot foiled or having your political group called out as the nefarious puppetteers that they are can open up entirely new avenues of roleplay and character growth for you and also gives a win to the other team.
Allowing the chance for others to come out on top is important, if your little friendship groups stomps on everyone repeatedly, you may find yourself with no one to play with.
To leave a papertrail or not is up to you, whether you conduct your business behind masks in shadowed caverns or via a sterile and safe chat medium is your choice. But perhaps don't make yourself infallible, many of our MMORPG's don't have an end game where the credits roll. When there is no defined win, take some chances and roll the dice.
If you've ever thought, "I'd like to try something different." If you want to step into a world where things are conducted in game, where planning out-of-character is discouraged, why not try a free to play MUD, like one of the great realms offered by Iron Realms Entertainment.