I'm typesetting a manuscript that is required to turn all \emph into underlines. But then I want to use the original definition of \emph for the list of references. How do I get \emph to behave like normal again?

Declare \normalem at the appropriate point in the document body. (The correspondent macro to switch to "underlined" emphasis is \ULforem.)

\documentclass{article}

\usepackage{ulem}

\begin{document}

Some \emph{emphasised} text.

\normalem

Some \emph{emphasised} text.

\ULforem

Some \emph{emphasised} text.

\end{document}

Another solution found in the manual is to use the \usepackage option [normalem]. This is probably a better solution if you are using the package ulem just for line struck through word or some other feature, but want you use \emph as italics. I know this is not exactly your case, but may be useful for someone else.