I just finished QfG1 (EGA) as a thief, and from the start I noticed how easy it was to max Throwing by just chucking rocks at nothing. However, even with 100 Throwing and Agility, I can't seem to do any damage with rocks or daggers. Cheetaurs are unfazed by them, and I burnt through my entire supply without killing Brutus. The only use I ever managed to get out of it was retrieving the spirea seed and deterring a saurus from attacking me on occasion.

So, continuing onto the rest of the series, is Throwing going to actually be of use, or should I stick to the Weapon Use & Dodging that served me well so far?

As a Thief, your best bet is to sneak past monsters. Failing that, Weapon Use and Dodge are more useful in combat than Throwing.

There are some puzzles that require you to have decent Throwing skill, such as the Spirea Seed puzzle (although, to be honest, a Thief can use Climbing to solve that particular puzzle instead). Later in the series, you'll encounter more of them, although I'd rather not spoil the other games by going into more detail about them.

In short: For avoiding combat, use Stealth. For combat, use Weapon and Dodge. For puzzles, use Throwing or Climbing.

The only exception I can think of off-hand would be the ogre outside the kobold's cave, since he's slow enough that you can do end-runs around him while you pelt him with rocks or daggers. I don't think any other monster is slow enough that you can do that.

So Throwing is never going to do useful damage to an enemy? Seems odd then that so many people recommend carrying extra daggers.

The ogre was easy enough to take down normally, since he's slow in combat as well. I was really hoping Throwing would be good against worthwhile enemies like cheetaurs, but oh well.

Well like I said, in QfG1 I threw a good 10 daggers at the brigand Brutus without coming close to killing him, and serious enemies like cheetaurs never had a scratch on them when combat started, and all of this with 100 skill.

I'm into QfG3 now, however, and the throwing daggers are finally starting to pay off. I can hit maybe half a dozen times before they get in range, and it actually lowers the enemy's health bar noticeably.