When someone sneezes I try say "gesundheit". Which apparently means "health". It's a common alternative so no one looks at you weird. Though, out of habit, i do catch myself saying "bless you". But, honestly, I think the religious connotation has been largely removed from sneezing enough that it doesn't matter too much..
In regards to saying something other than "bless you". In the anime Cowboy Bebop one of the characters sneezes and the other character says "take care". I like that because it removes the religious connotations, but still wishes them well.
In terms of substitutes to "bless you," I'm fond of the Spanish "Salud," which translates literally into "Health."
Thanks! According to this Wikipedia article, many other languages use some variation of “To your health,” rather than a blessing.