Let's start with Java. Probably security issues have been addressed to a greater extent in Java than in any other programming language, and many unusual design decisions are due to security concerns. However, platform-independence (i.e. portability) is another major force driving the design of Java, and it motivates the decision to implement by interpretation on an abstract machine. The concerns for security and portability are in turn motivated by use of the language over the internet, as are threads for (psuedo-)concurrent execution. APIs allow portability without sacrificing functionality, and in particular provide extensive support for interactive graphics, which again is motivated by how the web is used.
The "ML" in HTML is for "Markup Language" not "Meta Language" as in the ML programming language, and HTML is not a programming language, but a language for describing multimedia content, originally in a way that is independent of the display device to be used, though later evolution of the language introduced many features to help graphic designers produce more pleasing layout for specific browsers. It would be interesting to survey all the effects that commercial competition had on HTML, but let it suffice to note that both Microsoft and Netscape introduced non-standard features in an attempt to lock-in customers. This was (and is) not good for users.
Perl fills a small but important niche in the internet world; it has many features that make it unsuitable for general purpose programming, such as being untyped and having weak modularity. But it is ideal for quickly writing relatively small translators, for example, into SQL, and it has therefore been called "the duct tape of the internet." It is also notable that Perl is an open source effort, and has very high quality implementations and documentation. See Perl: The first postmodern computer language, by Larry Wall, the designer of Perl, for an amusing discussion. What is most interesting about that paper is not its content (which is a bit shallow and self-serving) but its style, which reflects a culture radically different from that associated (for example) with Ada or COBOL, which were designed and built with military sponsorship. Wall is part of so-called "hacker culture," which tends towards doing "stuff `cause its cool," i.e., for fun, as opposed to defense contractor culture, which by necessity is more serious, since it builds software for systems that can kill people.
As a linguistic note, the word "hacker" has been around at least since the 1960s with a meaning like that discussed above, but was "hijacked" in the 1990s by the media and given the radically different meaning of someone who does illegal and/or unethical programming. The original usage appeared in the MIT AI Lab, along with many other amusing words and phrases, during a time of great excitement, exploration, wealth, and productivity. For example, "frobnicator" is a rough synonym for "hacker" (though without the connotation of high skill), derived from the verb "frob," which means to fool around with something, with no particular goal. For more (much more!) on hacker language, see the Jargon File. I find it encouraging that there is a healthy computer science subculture that is freedom-oriented, public spirited, and somewhat rebellious (promoting open source software), in contrast to the culture of greed, which Microsoft seems to exemplify.
I suggest that you now re-read the Preliminary Essay on Comparative Programming Linguistics, for its discussion of how intent and social context affect design. A major part of the social context for these languages is the commercial use of the world wide web, and the competition between MicroSoft and nearly everyone else, to provide software to support this. Another clash of note is that between the open source movement and the business culture.
For an overview which includes some historical information as well as the usual technical information, see Programming the World Wide Web, by Robert Sebesta, Addison Wesley, 2002; there is nothing deep or original here, but you can get a feel for the current state of play.