Since you say you have had a great deal of rain lately, and standing water, these could just be what would develop as roots if that part of the plant was in contact with or under ground. I don't always stake or cage some tomatos and they will form roots where they fall over and touch the soil. It can sometimes be an early signal of some root problems but is usually just the natural response to wet conditions.Some of the worst plants have what I'd compare to a rash on it's stems. Bumps really, not discolored bumps, but is this part of the problem also?