Take it from someone who has done tons with eCommerce and written several solutions. In my opinion, PHP or Perl is the two languages you should go with. Either are native to linux and can do basically anything on either. There are people who argue that Perl is a whole lot more powerful than PHP but I'm one to argue against it. I feel that PHP, now that it is in v5 has become a very powerful tool. I have integrated back-end payment systems with PayPal.com software for the occasional online marketer, I've also overseen several major overhaul projects that utilized larger companies such as connecting to Visa and Mastercard directly along with Authorize.net servers.
My language of choice is PHP although I have no problem with Perl. Moral of the story is, use a language you are comfortable with. If you do JavaScript programming, PHP is not a far step away, mostly function name changes and minor syntax. If you are a C/C++ programmer, you basically can go to any one you wish. If you are new, PHP or Perl. Perl is a little more complicated but once you get the hang of it, it's not too bad. Reserve Java for later unless you really wanna dive in. Java isn't complicated, you just have to know the manuals and where each function is located. It's a very intertwined language. If you've looked at C# you've basically looked at Java as MSJ++ and MSC# were both based toward how Java organizes everything.