www.askdrsears.com
check for any discomforts he may have. check to see if it isnt too hot or too cold. check to see if he just needs more physical contact. make sure his diaper isnt too small or too tight... it would leave imprints... check for any rashes on the skin, a sliver or something,
if all else fails, take him to the doctor to eliminate any chance of ear infection or other pain that way....
good luck. im glad that you are sensitive to your baby's needs to not make him cry it out. check the website i mentioned for information on cry it out, and be glad you are strong enough to listen to your intuition. you are being told something is bothering your son, and thats a GREAT thing~!! :D