Not quite sure I follow.
What's the main difference between:
あなたのめがきれいです
あなたのめはきれいです
In this particular example, I don't think either of these constructions would be very natural. When talking about someone's body parts, the usual form is to identify the person as the topic with は and then the specific body part as the subject with が.
So in this case it would be あなたはめがきれいです。
(Of course there's also the issue that you shouldn't generally use あなた to address someone unless there's no other option, but that's a whole different subject. In example sentences like this, it's totally fine.)
In general, though, it's true that the は/が distinction can result in different kinds of emphasis. One way I've often heard the distinction described is that a は sentence and a が sentence are answering different hypothetical questions. So to give a basic example:
1) わたしは にほんに いきました。
2) わたしが にほんに いきました。
The first sentence could be used to answer the question "Where did you go?" (あなたはどこにいきましたか
or "What did you do?" (あなたはなにをしましたか
. The "I" doesn't really get any emphasis because it's the topic (and indeed could easily be omitted from the sentence entirely in many contexts). The emphasis is on what was done.
The second sentence could be used to answer the question "Who went to Japan?" (だれがにほんにいきましたか
So the emphasis is roughly "
I went to Japan."
But this emphasis isn't necessarily very strong or even present in all cases where が is used. It's all a matter of looking at the context. For instance, looking at the above あなたはめがきれいです sentence, it could indeed be a response to a question of わたしはどこがきれいですか ("What part of me is beautiful?"), but more generally, the が is used because you already have a topic marked with は and you're narrowing it down to talk about a specific part of it. It's very neutral, and definitely wouldn't carry any implications that you think other parts of her aren't attractive. The overall topic, after all, is still the person as a whole.
In fact, confusingly enough, if you were to say あなたはめはきれいです,
that could definitely carry an implication that you don't think any other part of her is beautiful. That's because when you specifically mark a topic where it's not necessary, there's usually an implication that you're comparing it to other possible topics. Like if you were having a conversation about dogs and everybody was saying how much they loved them, you could say わたしはきらいです ("Me, I hate them.") The explicit わたしは draws a contrast with the other people who were saying the opposite. In a similar way, the explicit めは in めはきれいです sounds like it's very specifically picking out the eyes to talk about, with the implication that you don't think the rest is worth mentioning.
I think the good old method of over-literal translation, by translating は with one of the rare English constructions that explicitly marks out a topic ("As for...", "On the subject of...", or "subject followed by comma") can help to make some of these distinctions clearer. So:
わたしはにほんにいきました "Me, I went to Japan." (I don't know where you guys went, but I went to
Japan!)
わたしがにほんにいきました "
I went to Japan." (Who went to Japan? It was me!)
あなたはめがきれいです "As for you, your eyes are beautiful." (What a charmer.)
あなたはめはきれいです "Speaking of you, as for your
eyes, they're beautiful." (The rest of you, not so much.)
いぬはすきなんですよね! "Dogs, don't you just love them?!"
わたしはきらいです。 "Me, I hate them."