This paper from Brazil has confirmed that organic tomatoes are better.
The study found that vitamin C levels were 50% higher in organic tomatoes and that phenols were up to 139% higher. Phenols are thought to be significant in halting degenerative diseases and in their anti-cancer properties.
The authors have hypothesized that the higher nutrient content is attributed to the higher stress levels that organic crops are subjected to. The payoff seems to be that the organic fruits were smaller than the conventional.
These findings are consistent with my own experience as an organic farmer. I have found that my lettuce is smaller than comparable conventional lettuce, but is tastier and has a superior shelf life. The Brandywine tomatoes pictured above were the most delicious I have ever tasted but I had no conventional Brandywines to compare them with. They however knocked the socks off supermarket tomatoes.