Using the \widetilde command to denote a tilde on a letter usually works wonders, although the tilde needs to be slightly lowered in my opinion. This didn't bother me too terribly until I needed to use it in a superscript:
Is there some way to lower the tilde sign in LyX? The \tilde command is lower in superscripts (although still too high in the rest of the equation) but provides an unsatisfactory tilde.