Seems the proper way to do it is use a comma:
<a href="https://stackoverflow.com/questions/9482633/tel:441234567,88">+44-1234-567 ext.88</a>
Just tested with iPhone and Android OS 2.1. Using ;ext=88 converts the ext bit into a number that is dialed with the extension (so it dials something like 35888 instead of 88).