JScript .NET (174 characters)
A little-known programming language from Microsoft, it combines the (relative) terseness of JavaScript with the power of the .NET Common Language Runtime. Thanks minitech and Joey for Console.Beep.
This program accepts a single letter from standard input (A-Z or a-z only). It does not explicitly add intra-character pauses, but they do exist, at least on Windows 7.
morse.js
function S(a){K.Beep(750,!!(a&C)*99+50)}import System;var K=Console,C=1<<26-K.Read()%32,A=31313855&C,B=60257815&C;S(29932103);(A||B)&&S(34172681);A&&S(9538602);A&&B&&S(66070)
Compile with:
%SystemRoot%\Microsoft.NET\Framework\v4.0.30319\jsc morse.js