I've seen diacritics corresponding to tones (in tonal languages), but asides from that I haven't come across a system for transcribing prosody in my studies. Is there a popular convention people use?
To my knowledge as of now there is no united way of transcribing prosodic features of language; however the need for one is critical and therefore there are several meetings being held for designing IPrA (internation prosodic alphabet) (ucla page for the description of the meetings)
This proposal is going to transcribe prosodic events at the "categorical phonetic" level of AM. For more details you can visit BU page for the meetings
Also you can see my question here