In casual conversation, 밥 먹었어? is the most natural one. 1. 을 is object particle so it is put after object of a sentence. And the 밥 here is the object referring to eat "what". But in casual conversation, the object particle is dropped a lot when it is clear enough without marking the object particle. So, that's why 밥 먹었어 is the most natural. Nobody says 밥을 먹었어 because it's super clear without the particle. 2. Then, when to put the object particle? 1) when it may not be so clear on which one is object in a prolonged sentence for example. 2) or in formal situations like news reporting, presentation, documentation, etc. (But 밥을 먹었어 is still not natural even in formal situation) 3) or when you wanna emphasize what the object is. For example when you specifically ask about the 밥, not others like coffee, bread, etc. 3. 은 has two functions, basic function and special function. As 은 was used after the object, it means the 은 here was used in its special function, which is for contrast or comparison. So 밥은 먹었어 here can be in contrast to other thing or situations with having some meaning behind. So when you ask this question in contrast or comparison to another, you can use this. For example, - Have you eaten? (Because you look like you haven't eaten anything) - Have you eaten? (Because you look like you've eaten something (in comparison to other food)) - Have you eaten? (Because I finished my first question about the weather, so then it’s my second question about the meal (in comparison to the first question) when you change the topic) For more details of 은, the below video may help you more: https://youtu.be/mnURCy8vt5E