From the official Skype blog:
Earlier this year we announced improvements that would reduce some of the noise – specifically synchronizing read messages across multiple devices – and today we are pleased to announce the next step in our journey to offer the best possible Skype experience across all devices. 'Active endpoint' is a new feature designed to only deliver chat notifications to the device that you’re currently using.
If you are signed in to Skype on multiple devices (a laptop, tablet and a smartphone) and you are sending chat messages to a group of friends from your tablet. Skype will only send new message notifications to your tablet and not to any of your other devices. All of your other devices will remain blissfully silent. You can continue to focus on the most important thing, your conversations, without being disturbed by the bleeping and buzzing from all of your other devices.
The moment you stop actively using Skype on any device, all devices will receive notifications again to make sure you never miss anything important. When you pick up any one of your devices to respond, we will stop send notifications to all other devices. Call notifications are still sent to all devices so you can answer on whichever gadget you prefer, not just the one you’re closest to.
Though the delivery of notifications is targeted and personalized to your own device usage, your chat history continues to sync across all devices allowing you to continue a conversation from any one of them.
We are currently rolling the active endpoint enhancement over the next few weeks so you should notice (or not notice ☺) this new feature soon.
In other words, intelligence is used on Skype's servers, to detect how long it is since you last sent a chat message (IM) and from which device. If within a certain timeout period (probably of the order of a few minutes), it's considered that you're engaged in a conversation on a particular computer/handset and notifications only sound on that device. If outside the timeout period, it's assumed that you've put the device down and notifications then sound on all signed-in devices.
Sounds good. The Windows Phone Skype client is updated fairly often, though it's not yet known whether the current version in the Store is fully compatible with 'Active endpoint'. Still, a good step from the Microsoft-owned company.