Can't help with smoking-friendly restaurants -- your best bet is a cigar shop with a smoking lounge. At best, they'll serve wine by the glass, as far as I know.
For a good dinner, I'd very easily recommend Ad Hoc in Yountville (near Napa), which is a terrific place by the same chef as the French Laundry, and it's possible to get in without too many reservation gymnastics. Menu changes daily.
For a nice lunch, check out Tra Vigne in St. Helena. Get the mozzarella al minuto, which is fabulous.