As upgrading Prototype has the potential to break a lot of things in Magento it is wise to create a theme override for the
file and include the following as the first element under the head tag:
<meta http-equiv="X-UA-Compatible" content="IE=8" />
This tells IE to pretend as if it is IE 8, where possible. This solved an issue where, for example, you could not check out and complete the payment process if you only have one payment method enabled, as in IE 9 the fields will all be greyed out.
Note that it really must be the first tag underneath the <head>.
Since upgrading Magento in any way has the potential to cause problems, it is the least intrusive way to solve the issue in the near term.