I was re-reading NHK ni Youkoso the other day and it struck me how contemporary it was, even though it was written in ~2001. Part of it is because he doesn't ever mention any specific series.
By the way, if you're going to read it I recommend the novel first. It's not particularly well-written, but the prose is still much more readable than typical light novels'. It's also more realistic in some parts. Between the manga and anime it's a toss-up but the latter is more popular. They're very different anyway.
There's also a list of games with hikikomori protagonists on VNDB (http://vndb.org/i720), but I'm pretty sure the only translated one worth giving a shot is Chaos;Head.