Generally, they're all a nuisance, especially when done en masse (see someone's earlier post about Malboro Bad Breath), but generally it's the game mechanics surrounding said afflictions.
In Final Fantasy, it's usually Mute/Silence and Berserk that have me banging my head. Stone and Death are a nuisance and Poison is a "meh" unless things are down to the wire. Unfortunately, there's been too many times when Mute or Berserk have come into play and made a bad situation worse for me.
I've played some other games where the status effects are almost non-existent and not inconvenient at all - thus ruining the point.
I'd have to say that in any D&D games (Baldur's Gate, Neverwinter Nights, etc), any status effect poses a serious threat, regardless of how stupid it might seem.
Blah, I've said too much... *uses "Invis Edge"*