Does anyone know if their is a way to edit multiple html pages while they are on the server in an easy, efficient way? I just need to add a small link to the bottom of all of my pages, but I have thousands and thousands of pages.

try using a server side language such as php. what you could do is create a template system. where you call a header, and a footer. and the header is such as "header.html" and footer is such as "Footer.html". that way you only have to edit one file and the whole site would be updated.

Would this require alteration of any of the actual html of the other pages?

yeah so you'd still need to update all of your pages

no other way though...

as said, unless you used SSI (Server Side Includes) originally you have to edit every one

Now sounds like a good time to start converting to SSI though

Some webhost accounts will allow you to generate headers/footers by the server. Check out all the features in your account control panel and see if it includes a feature for server generated content.