1. Well, you could always go for the italicization route, where you just italicize the words to show that the sentence is being said in a language foreign to what the main characters are speaking in. You could also just emphasize that the sentence was spoken in another language. I've never really heard of a specific method for Pokemon, but there isn't anything stopping you from making your own.
2. The best way to show a song is to put it into a format similar to poetry. Center the text and make sure the stanzas are where they need to be. Let it be noted that these should be italicized, or at least they usually are.
3. A character shows emotion in many ways. There is body language, vocal tensity, physical motions -- there is an endless vector of how emotion is shown, especially in prose. Even the flicker of an eye can tell you a lot, and that's where you will have to be very detailed. "Ghetsis' eyes flared across the room, slamming his sword deep into the cracks of the ground as he shunted an accusing finger at the hero. His gritted teeth seemed to translate into reality as the earth rumbled deeply, and the beast of his efforts erupted from the wall behind him. . ." etc. etc. I could have done a better example, but I don't often write fan fictions, especially Pokemon ones.
There are plenty of ways to do that. For example, in a book series called Animorphs, the main characters could transform into animals and talk to each other telepathically. The author showed which messages were 'translated' from the telepathic language by replacing quote marks with <these>. There's no reason why you couldn't do the same thing for Pokémon talk.