From what I read earlier, 君【きみ】 can be used for "you". But in many instances over the Internet, I have seen キミ being used instead of 君【きみ】. What is the usage difference between the two?
If I take the following sentence for example
ちょっと、そこのきみ！
which means "Hey, you there!"
Can it be written as both
ちょっと、そこの君！
ちょっと、そこのキミ！
Choice of script in Japanese writing is often a stylistic attempt by a writer to convey some non-standard subliminal meaning. There have been some interesting analyses on this topic done over the years. Just to give you an idea of some of the findings, one study found that certain characteristics were often attributed to script usage, as follows:
Hiragana: feminine, soft, smooth, round, tender, simple, childish, lovely, elegant, etc.
Katakana: novel, foreign, emphasizing, hard, fake, male, futuristic, sharp, jarring, angular, etc.
Kanji: scientific, rigid, masculine, formal, hard, difficult, intellectual, visual, substantial, etc.
It’s clear that 君 is usually written in kanji, so a writer’s decision to use キミ would definitely be an attempt to inject something different into the ‘tone’ of the word. In your example, perhaps it is an extra sense of irritation that the writer is trying to express. Or maybe a sense of urgency. The point is, deciding to use a script which is not conventional is a way to infer different layers of meaning. What that meaning is can depend on things like the writer's intention, the context, the characters, etc.
The difference is very small, and this is basically up to the writer's taste. I somehow feel キミ tends to be preferred in some recent "light" novels, but this is far from a rule.
See: Why are katakana preferred over hiragana or kanji sometimes?
Difference between the usage of 君 and キミ
It depends where they are used.
In Japanese, there are several ways of writing a word like in hiragana, katakana and kanji as is asked by the questioner for the way of writing "kimi".
The type of characters depends largely on in what kind of sentences "kimi" will be written. The closer to the formal sentence the less freedom of choice becomes, and in that case "kimi" is usually written as "君" in kanji.
Next, in case of personal sentences used in the network or sentences of novelists where the expression method is free, the type of characters depend largely on that placed before and after "kimi" rather than how to express the writer's intention by them.
(1) ちょっと、そこのきみ！
As you know, there is no space between words in written Japanese sentences, unlike English. Therefore, it is most important for the writer to properly use the type of characters so that the reader can easily parse the sentence without misreadings as is intended by the writer.
In this sense, the sentence with (1) would not be evaluated highly in selecting the type of characters for expressing "kimi" because for even a native speaker of Japanese, it is not easy to parse "そこのきみ" of 5 characters in hiragana in a moment.
(2) ちょっと、そこの君！
(3) ちょっと、そこのキミ！
From the viewpoint of recognizing the word "kimi" in the phrase, both (2) and (3) are much better than (1).
In general, "ちょっと、そこのkimi！" is not used so much because it has a nuance that the speaker of the phrase seems arrogant or bossy.
I have an impression that (2) is more common and (3) is like an expression used within friends. Therefore, I think it is reasonable for the questioner to say that he/she has seen キミ many times on the Internet.
