Someone posted a link to this site on the Bioware forums, and I seen this topic, so I just had to post myself.
Mage vs Thief
A mage will win this battle if, and only if they use a chain contingency: abi dalzims x3 on hit, with the target being last hit by. 3 flame arrows might do it too. For either spell, the mage better hope that they inflict as much damage as possible, and that the thief doesn't make any saves and hope that he's not wearing the girdle of inertial barrier. Otherwise a thief even without HLA's will have no problems at all. If a mage gates a demon, thief runs away until it's unsummoned. If the mage goes invisible, thief drinks a potion of invisibility, and detects illusions without coming out of invisibility. As soon as a mage starts casting true sight, the thief runs away, then comes back hiding in shadows while already wearing the cloak of non-detection naturally. To get the stoneskins down, every thief will be carrying a few arrows of dispelling on them, and will be just barely in range, so that they can run away before the mage gets a power word stun off. Once all the stoneskins are down, thief makes a backstab and the game is over.
Fighter vs Thief
No contest, even if the fighter is wearing something that makes them immune to backstab. All the thief has to do is keep drinking invisibility potions until the fighter is dead, and there's more than enough of those in ToB. Invisibility potions work so quickly after an attack, that the fighter will never get a chance to make a swing. The fighter can easily drink invisibility potions, but they're just as quickly dispelled with the thief's detect illusions.
And that's all without a thief using a single HLA. If you want to use HLA cheese, a thief can just summon nishruus or hakeashars and eat all of the mages spells.