I suspect you had septoria leaf spot. This fungus lives in the soil. It is carried by water splashing from the ground on to a leaf carrying the spores with it. Then it splashes from leaf to leaf until the whole plant is effected. It does not effect the tomatoes just the plant's leaves so the seeds are fine.

Clean up any fallen leaves and destroy them and the plants. Do not compost them. The disease keeps going as long as the leaves can carry the spores back to the soil. It is likely to be there next year too as it's hard to get rid of. Pick off the bottom leaves if you see it. You can also spread black plastic over where you plant them and cut small x's in it to plant your tomatoes. If the fungus can't get to the leaves they can't be effected. The plastic will also solarize the soil and perhaps kill the virus

Might want to also ask over on the Growing Tomatoes forum.

Rodney