My guess is they're just overripe, which is not a bad thing for seeds.

Unless you're selling seeds, I don't see any bad thing happening from keeping those seeds. Worst case they will not sprout when planted.

Seed born diseases are very rare (I read, never seen myself). On the other hand, tomatoes have a lot of seeds :P

So unless someone gave you just one tomato and you want to save as many seeds as you can, I'd just go with "when in doubt, throw it out" theory ;)