Dealing with distractions is a fundamental rule to a successful project. Skype is a great way to get distracted. Following these options helps you to minimize messaging/communication distractions:
Set your status to Busy - people will think twice before messaging you
Don't display an alert when a contact comes online or goes offline
Don't play a sound when you receive an email. Remember - you do need a sound when you receive an IM in case you're not looking at your PC when it arrives
Figure: Minimize Skype alerts you receive