I wouldn't worry much about MP3 right now. All of the remaining patents related to MP3 are going to be expired in 2017, and it's widely recognized that Ogg Vorbis is better; MP3 is used only for compatibility. The audio format which can cause problems in the future is AAC, and as far as I can tell, it hasn't seen particularly widespread adoption on its own (the only adoption I've seen of AAC is in video containers).

Right now, the formats most likely to cause problems are video formats.

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