We've done this in several skins. The JavaScript is probably the best method but the link element works as well. When we use the JavaScript method, we add it to a script file where we store all of the javascript we create for a single site. That script is then added to the layout.master using the portal:SkinFolderScript control with the AddToCombinedScript="true" property set. This will help with the page size and load which can have a positive effect on site speed.

HTH,
Joe D. 

It's best to store your skin specific scripts with the skin. When you use the AddToCombinedScript parameter, it keeps there from being yet another file downloaded by the browser.

The upside of using services like Google Web Fonts is that the files are on a CDN so as more people use the service, the better the chance is that the fonts will already be cached when a user loads your site. Also, the Google Web Fonts service allows you to imbed the fonts using a link element if you don't like the JavaScript option. Again, this allows use of the CDN which is generally going to be a lot faster than any shared hosting server.

To use the script loader to load your JS with the combined site script, do the following:

1. Create a new js file in your skin directory, I usually name it skinscript.js.
2. Add your javascript to the new file. Don't use <script> tags, you don't need them in javascript files.
3. Add <portal:SkinFolderScript ID="sfs1" runat="server" ScriptFileName="skinscript.js" AddToCombinedScript="true" /> to your layout.master. I usually add this right after the <asp:ScriptManager control.

You can move the scripts in your layout.master to this new js file but it may take a little bit of trial-and-error because depending on how they were written, they might not work properly being lumped together. We always add the toolbar and superfish scripts to this file and we don't have any problem with them.

HTH,
Joe D.