In the 10th Doctor episode, The Runaway Bride, the Doctor says:
Ahh! The wedding! That's right, you're getting married! That's it! Best day of your life, walking down the aisle... Oh, your body's a battleground, there's a chemical war inside! Adrenaline, acetylcholine, wham go the endorphins! You're cooking! Yeah! You're like a walking oven, a press cooker, a microwave, all churning away; the buttons reach boiling point and shazzam...
I think that part of this would suit a wedding card, perhaps even as a reference rather than a direct quotation (in the same way that their reference was subtle). In your message, mention adrenaline, acetylcholine, and endorphins; perhaps suggest that they'll enjoy their new oven, press cooker, and microwave (but they should be careful when reaching boiling point). It seems like you could work that into an otherwise normal message, but the astute Doctor Who fan would catch that this was a reference.
There's another reference to marriage in the 11th Doctor episode, The Big Bang:
DOCTOR: Are you married, River?
RIVER: Are you asking?
DOCTOR: No. Hang on. Did you think I was asking you to marry me or asking if you were married?
DOCTOR: No, but was that yes or yes?
It's harder to see how you could work this into the card, unless it was just a plain quotation. If their proposal was anything like this, then perhaps it would be suitable.
Although weddings and marriage occasionally came up with Doctors 1 through 7 (e.g. several companions married when they left the Doctor), I cannot recall or find any good quotes about marriage or weddings from these episodes.