I've run across this problem in a number of different contexts, and usually the cause is the simplest thing for which you could look.
All these other solutions posted could weed out more complex and weird causes, but in my experience (six years as an IT manager) it is best to go with Occam's Razor*:
There's something funky going on with your speakers or your sound card.
It is unlikely that a weird sound coming from your machine was caused by an application that otherwise keeps its lips shut. And Windows sounds are pretty trouble-free.
- Brian
*
For those of you who have an urge to Google here . . . "Occam's razor is a logical principle attributed to the mediaeval philosopher William of Occam (or Ockham). The principle states that one should not make more assumptions than the minimum needed. This principle is often called the principle of parsimony. It underlies all scientific modelling and theory building. It admonishes us to choose from a set of otherwise equivalent models of a given phenomenon the simplest one." -- from the Principia Cybernetica
