I saw over the interweb a lot of possible solutions javascript solutions, meta tags, css and maybe I found an hack actually working for my websites, I tested on some computers and it work and I think it will work until skype don't change something in their code.
I was looking what is the skype exactly doing on our pages, and it creates some span around the phone numbers, as you already said, but it even add an <object>
tag at the end of the document, just after the body closed tag.
And here I saw the trick! Just before that object there is a configuration tag:
<span id="skype_highlighting_settings" display="none" autoextractnumbers="1"></span>
This is added dynamically by the plugin! but here the solution become obvious, to finally stop skype messing with your design and avoid changing phone number the solution is to insert very early in the document the following tag:
<span id="skype_highlighting_settings" display="none" autoextractnumbers="0"></span>
notice the autoextractnumbers="0", here is the trick. The document will not validate anyway with that tag because there is no attribute "autoextractnumbers" but i noticed that it works even if commented:
<!-- <span id="skype_highlighting_settings" display="none" autoextractnumbers="0"></span> -->
And that's it! Enjoy your webpages free from messy plugins! And your web page will still validate correctly. Hope it works for you too! I have tested on a couple of computer 3 different browsers and 2 different skype versions, for now it works for me, let me know if it works for you too and if it works share it :)