I've seen stutters written with hyphens, such as "Bu- bu-bu- but I- I-I- I- I n- n-need you!", with spacing indicating pauses and how long they last.
For somebody clearing their throat, all I've written was "He cleared his throat before speaking." Same with hoarseness; just indicate in the dialogue "Her voice was hoarse" or something similar.
Pitch, tone, and rhythm/cadence can get a bit more descriptive. You couldn't write it in the actual dialogue; you'd need to describe the actual tone somebody was using: "His tone suggested she needed to put the files down and leave immediately." "'What are you doing?' she screamed, her pitch scaring dogs three counties away." "The professor's monotonous speech had everybody asleep within fifteen minutes of the lecture's start."
