Taken from an article from the american egg board
"...One of several types of bacteria which can cause food poisoning (salmonellosis) if ingested in large numbers. It is found in the intestinal tract of animals, birds, insects, reptiles, seafood and people. The bacteria can easily be passed from the intestinal tract to the hands and onto the food.

Although the inside of the egg was once considered almost sterile, Salmonella enteritidis (Se) has been found recently inside a small number of eggs (much less than 1%). If an egg does contain Se, the numbers in a freshly laid egg will probably be small and, if the eggs are properly refrigerated, will not multiply enough to cause illness in a healthy person.

The majority of salmonellosis outbreaks have been attributed to foods other than eggs - chicken, beef, and fish - to human carriers, and through them, utensils and other goods during preparation. Of the outbreaks involving eggs, almost all have occured in the food service sector and have been the result of inadequate refrigeration and insufficient cooking. Se will not grow at temperatures below 40 F, and is killed at 160 F...."

www.mercola.com/2002/nov/13/eggs.htm
www.mercola.com/2003/feb/5/eggs_salmonella.htm

I've read a lot more but those were the quickets things I could find at the moment. But really, If you're not comfortable don't do it. I'm 100% comfortable and I do...but am not on an egg campaign here, just saying that I DO eat them soft and or raw and am happy to do so.

In the cookbook I have "Nourishing Traditions" by sally fallon and the lady who wrote "know your fats" they actually recommend for babies 4 mos or 1 year (I forget) and older to eat the yolk only of a soft boiled egg daily. (the whites are not easily digested). Before getting pregnant I ate a LOT of raw food.. tons of raw meat/fish, milk, eggs and cheese... now I'm just on the eggs until after the birth.

btw: I get eggs fresh from the farm when I can get them, otherwise it's the good ones from local stores - I would never eat the sick looking ones with pale yellow deflated yolks from walmart or other huge stores that have been sitting there for ages and touched by God knows who.