By default Skype should always leave and display text as it was typed
Trust people to know what they are doing, and transfer text the way it was typed, and display it so it looks exactly like it looked on the senders side.
Text coming from the clipboard, or being dragged onto a contact or the send message text box should also be treated this way. The text should look the same on the receiver side as it would look if it were pasted into notepad.exe.
Smilies and shit should be an opt in option, for all sake, do a huge poput the first time you encounter something that you believe could be converted to a smiley and ask if the user want his text to be messed with or not.
No matter what, all conversions should be done on the senders side only. Under no circumstances should the receiver get something else than what the sender was looking at before he pressed send.
There should be a right click option to revert any auto conversions done with the text.
Also, I think that the choice to use parentheses to indicate emoji and special Skype symbols was a poor one. These occur frequently in ordinary text. There would be far fewer problems if emoji replacement happened on keywords surrounded by braces, for instance, rather than ones surrounded by parentheses as now. There should also be an OBVIOUS way to prevent replacement of any kind. For instance a "Verbatim Chat" selection with on the main screen or when composing a message for sending, with three options: "Verbatim", "Replace text with emojis", and "Ask. but only if any replaceable text appears to be present".
I always love it when Skype turns my code into smilies! Makes life so much more interesting.