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PHP

PHP was the first open-source language designed for the web and reached maturity around 1999 with the release of PHP4.  Before PHP there was only Perl (free, but a general-purpose scripting language, kind of hard to learn) and ASP (which was not free and required an enterprise-level budget to run.)  So PHP had a head start of about 6 years over Ruby andy Python.  (These languages existed since the mid-1990s but had no web frameworks written for them).

Despite PHP's many shortcomings (lack of true object orientation, weak exception handling, no lambdas, and as others have mentioned, is essentially a huge flat namespace of inconsistently-named functions) it won by its ubiquity.  It was free and even the cheapest commodity web hosting providers were offering PHP by 2002 or 2003, so it had a full generation in Internet years to establish itself as the common language for open source developers.  

The emergence of Rails in 2005 began to change that but it took a few years for Rails to gain mainstream acceptance.  Python followed suit with the development of the Django framework, on the same MVC pattern as Rails.  

Services like Heroku were essential in getting Ruby to the mainstream - you no longer needed to have dedicated servers or know how to compile source code to run a Ruby server - you essentially had the same consumer-level pricing for running Ruby apps that you had with PHP.  

Ruby and Python are overtaking PHP because developers tend to favor the languages - they have better abstractions and allow programmers to be more productive.  Also, the ubiquity of PHP worked against it a little because it meant that less-skilled programmers could contribute code and the quality of code in PHP projects is generally of much lower quality as a result (see WordPress plugins for example) while the Ruby and Python communities have focused on developing better coding practices like Test Driven Development.  As a result, people who use Ruby and Python are perceived as "better" programmers and more desirable hires.  New technology-focused companies are thus more likely to start projects in Ruby and Python because of the perceived higher quality of developers, even though for most web applications, an experienced team ("experienced" being the key) using Symfony or Cake can be just as productive as a team using Rails or Django

There's always going to be a fringe language X that's favored by hackers and academics, but has no obvious business application and thus stays obscure, only to seemingly come out of nowhere years after its invention when the critical mixture of a user need and practical libraries is achieved.  Today it might be Haskell or OCAML or Scala.  It's been LISP for about 50 years now. 

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