The custom of saying anything after a sneeze was begun literally as a blessing. Pope Gregory the Great (540-604 AD) ascended to the Papacy just in time for the start of the plague (his successor succumbed to it). Gregory (whom we can also credit with the ever-famous Gregorian chant) called for litanies, processions and unceasing prayer for God's help and intercession. Columns marched through the streets chanting, "Kyrie Eleison" (Greek for "Lord have mercy" and a huge hit for the 80's band Mister Mister). When someone sneezed, they were immediately blessed ("God bless you!") in the hope that they would not subsequently develop the plague. All that prayer apparently worked, judging by how quickly the plague of 590 AD diminished.
When I was a kid I was told that the reason you say anything to a sneezer is because when one sneezes, his/her heart stops, and you "bless" them so that their heart starts beating again. I have since learned that this explanation is to be filed in the same mental drawer as the Easter Bunny and Santa Claus (although the ruling is still out on the Tooth Fairy cause there are lot of gay men out there with great teeth).In Europe, it was believed that sneezing expels the soul--the "breath of life"--from the body. We know today, of course, that when you sneeze, your heart doesn't stop, nor will your eyes pop out if you can keep them open, nor does your soul get expelled. What does get expelled are hundreds upon thousands of microscopic germs speeding out of your nose at up to 100 miles per hour!
When I was in college, I did a study for a sociology course where I would go to certain locations and sneeze my best try-not-to-sound-too-fake sneeze. I made notes of the demographic and who was in my immediate vicinity. And out of those people, I made a chart of who blessed me, or said anything to me for that matter. I remember that it was mostly older people who said anything to me, most of the younger ones did not acknowledge me. I also recall that I was surprised that more people DID NOT bless me than DID. And it was something like 1 out of 8 who said "gesundheit" instead of "bless you". I was a bit limited in my ability to travel to different cities or states or countries to expand on my research (but then again, I had a life), so my outcomes may be skewed to regional colloquialisms rather than anything else.
I used to date a man who would sneeze three times in a row. I would bless him the first two times and after his third sneeze I told him he was one his own - I only bless twice. Within a few weeks, he was only sneezing twice. Coincidence?