1. Valuation of a property like Skype is a lot more than just some multiple of earnings.
Quite a few bloggers, twitterers, and forum participants jumped on Facebook, Google, and Microsoft for their billion-dollar valuations of Skype. Usually the criticism was based on Skype's lackluster earnings. This is a massively myopic point of view.
One can acquire a company for many reasons beyond its current revenue stream: the company may own resources that it is not adequately exploiting, such as technology or highly valuable personnel; it may have a valuable brand or a large user base (which is certainly true for Skype); it may have valuable information about its customers (again true for Skype as the communication graph -- not just the link graph -- is valuable); and finally, the company may have untapped revenue potential, just not with their current revenue model.
As a general rule, just because one cannot think of a way to monetize something, it doesn't mean that there is no way to monetize that thing.
Another possible reason to buy a company is strategy at a corporate level: to stop it from developing into a competitor for some of our products, to stop competitors from buying it (and therefore becoming better competitors), and to signal commitment to a specific market.
2. Perhaps there's a little Winner's Curse going on here, or perhaps not
When three companies (Google, Facebook, and Microsoft) compete for the same company, there's always the possibility of a little Winner's Curse effect:
Assume that the value of Skype to these companies includes a big fraction that is common, meaning that it will be realized independent of the owner. Call that true common value $v$. To simplify, for now, assume that there are no synergies or strategic advantages for any of the buying companies; so the whole value is $v$.
Using all the information available, Google, Facebook, and Microsoft estimate $v$, each coming up with a number: $\tilde v_G$, $\tilde v_F$, and $\tilde v_M$. Note that these are estimates of the same $v$, not a representation of different actual value that Skype might have for these three companies. The estimates are different because each company uses different financial models and has access to different information or weighs it differently.
In a competitive market the winner will be the company who has the highest estimate, so we can assume that $\tilde v_M > \tilde v_G$ and $\tilde v_M > \tilde v_F$. The question now becomes: is what Microsoft paid for Skype higher than $v$ (the true $v$)?
Probabilistically the winning $\tilde v$ is likely to be higher than $v$,* since it's the maximum of three unbiased estimates -- one hopes these three companies have good financial advisers -- of the true $v$. Microsoft knows this and may shade its offer down a little from $\tilde v_M$. But even so, there's a chance that it paid too much.
Except that we're ignoring all the non-common value: synergies, strategic fit with Microsoft's other properties, and signaling to the market that Microsoft isn't yet a zombie like IBM was in the '90s.
There's a lot going on between Skype and Microsoft that the online comentariat missed. Then again, that's the fun of reading it.
(Hey, I finally wrote a business post in this blog that I repositioned as a business blog over a month ago!)
* If the distribution of the errors in estimates of $v$ is symmetrical around zero (ergo the median of $\tilde v$ is $v$), the probability that the maximum of three observations $\tilde v$ is higher than $v$ is $7/8$.