Yep. Actually I even made a post with almost identical content to Qhimm's post to explain the thing, after I posted I found out that Qhimm had already explained it (with spoiler tag, I might add), so I removed that post.
Funny thing is that I have played Xenogears only for few minutes (it's one of the games I'm planning to play when I get around to it, whenever that's gonna be), but the hint was from the opening FMV.
As for the puzzle itself: it actually took only few minutes to solve, probably because I've seen similar before (and I got lucky). There's only limited number of ways these things can work, unless... After I solved the puzzle I was suspected that it had a pretty good chance of being Xenogears, because there are not that many games with so direct references to... you know. But I had to check it to be sure.
Oh question, question... I'll get back to you when I come up with something.
Should be reasonably soon.
EDIT: Behold, the question has arrived:
Nyevtug, anzr guvf byq CP tnzr:
- Lbh ner PVN'f ntrag Znk Erzvatgba
- Enaqbzyl trarengrq zvffvbaf
- Frireny 'fho-tnzrf', gung vapyhqr jvergnccvat (avpr oenva rkprepvfr, onfvpnyyl zrffvat jvgu ybtvp tngrf), qrpbqvat rapelcgrq zrffntrf (jurer qb lbh guvax gung V tbg gur vqrn?
, oernxvat vagb 'rarzl' fnsrubhfrf, cresbezvat fheiryynvapr ba gurz naq fb sbegu.