Well, here we go!
I’m answering from the perspective of “which had the most impact on you,” since “in your eyes” would make me try to answer as objectively as possible… but the result would just be too vague. Also, I’m not particularly convinced that I fully agree with what I’m saying here. That is, I may change my mind upon closer consideration, possibly even within hours of posting this! So if you’re looking for something a bit more… well-established… it may be better to simply skip this post.
As @Pepe pointed out in his post above, all of Key’s stories have powerful messages. It’s a bit difficult to narrow it down, with AIR and even Charlotte (!?!?) being considered. So for me, considering the other options closely, I’m going with Angel Beats!… wait wait, hear me out! There’s a good* reason for this!
*in (a baseless) theory, anyway
I’d consider the “message of Angel Beats!” to be an amalgamation of the various messages it presents, since they all seem to be under a vaguely common theme. That makes it pretty versatile, as anybody watching it has a good chance of finding something they can relate to, which then ties in with all of these other things.
The way I see it, Angel Beats!'s message could implicitly encompass the majority of other messages from Key’s works, and other works in general.
Regarding the anime presentation: For casual anime viewers, Angel Beats! is also, in my opinion (with some technicalities), pretty easy to get into compared to other Key works. That makes it easier to communicate the message, whether the viewer is fully aware of that or not.
In terms of actual measurable impact, there are definitely parts of the story that pretty much anybody can easily do (Angel Beats!, regarding Otonashi’s memory: organ donation).
All that said, I don’t really entirely agree with all of Angel Beats!'s message, as I’ve interpreted it anyhow. That’s another topic altogether though.
If I were to say which Key work delivered the message I liked the most, I’d say probably Rewrite, because:
^ that.
Little Busters! was a runner-up for most powerful message, but the “bad end” in Refrain wasn’t the “true end.” That’s another topic altogether, which I’ll save for the Little Busters! bookclub.
That! Yes, same here. I’m trying to discard that aspect when considering the various messages, but it’s not all that effective to do so, since it would mean reevaluating something highly subjective from a more objective view. :/