I will say "bless you" or "Gesundheit". I don't really care, and I don't think many people still associate it with its religious connotations now. It's just something people say when someone sneezes. In fact, I didn't even realize it had any religious meaning until I was about 12 or 13. Until then I thought it was a word that was spelled and pronounced like "bleshu". I actually still pronounce it like that. I never distinctly say "bless you". I just slur the two words together.
In any case, it's a harmless phrase that really just means the person is wishing you good health. I can't really get offended for that.
Of all of the things Christians do...of all of the problems that come out of religion...this is at the very bottom of the list. This is simply a habit people get into (Heck, even I say it sometimes...) - sure it's unnecessary, but it's born out of politeness - and most who say it are simply trying to be polite, not preachy.
I say "bless you" - I was raised to say it (not because my family was crazy god-fearing and wanted to bless everyone, just because it's what they think is polite). It's a hard habit to break, and I honestly don't even care to try to break it, it doesn't bother me at all. It's culture. I do get a bit offended if I'm talking about something in my life that is difficult and someone says "Well God bless you" or something like that, but that's definitely more religiously oriented.
I got out of the habit of saying bless you. instead i say salud. it's spanish for good health, but i don't get offended when people tell me bless you. i do get offended when people try to convince me that i'm wrong for being an atheist.
Naaah... "Bless You" could be easily interpreted as a person's wish for "good fortune" upon you. [Which could be considered a compliment. ^_^] - I get more offended when someone who finds out about my lack of belief says they'll "PRAY FOR ME." - ugh... like I need that! But... everyone's so used to saying "bless you" after you sneeze... that it really has no meaning anymore.