Can I exclude certain Keywords from being replaced?

Pretty Links does not support this capability natively, but there is a way to make this happen pretty easily.

If you enter the Text mode of your page or post when editing it, and replace a character in the word(s) you are not wanting replaced with the HTML ASCII value for that character, Pretty Links should not see it as a match, yet the word will still appear normally on the page.

You'll want to be sure to save the page while still in Text mode. If you go back to Normal mode then the TinyMCE WYSIWYG editor that WordPress uses will convert the ASCII character back to normal again.

So let's say you wanted to replace an “x” in the word Chemex. You would enter Text editing mode and find the instance of that word in the content you don't want replaced — and change it to Chemex. The x is the ASCII representation of the lower case “x” character. You can find a full reference here: http://www.w3schools.com/tags/ref_ascii.asp.