Yes, Java is a popular OSS language...
Matt, I must admit that I always take these "my code base is bigger than your code base" stats with a pinch of salt. It often depends on scope, on what code you reckon is important enough to count and how you count it, and I'm not sure how I'd go about coming up with anything definitive myself. Which is why I was vague on the exact numbers - and I don't think that the popularity of Java vs. C++ was the main point of the article anyway.
However, the source is http://www.google.com/Top/Computers/Programming/Languages/Open_Source/, if that helps. I think that this provides some metric for popularity, but I agree it doesn't necessarily equate to "most used". However, according to Fortify, it's very difficult to figure out how many OSS packages there are of any 'flavour' (SourceForge, I'm told, doesn't list major packages such as Apache, MySQL or Linux).
To put "popularity" in context, at the end of 2005 an Ovum analyst said "We estimate that there are over 200 billion lines of COBOL in production today, and this number continues to grow by between three and five percent a year” . Would that make COBOL a "popular" computing language?
As for what is an OSS language, Java and PHP feature in that Google directory reference bur COBOL doesn't. Is there a lot of OSS software written in COBOL? Probably not (but I'm now waiting for something like IBM to point out that there's a major COBOL OSS project on Aphaworks).