Among the community, I often see it joked that Halflings have access to an absurd number of bonuses to rock-throwing. This joke is undoubtedly based on the fluffy references to the importance of rock-throwing in their culture. But, in terms of rules, what benefits to rock-throwing do Halflings actually have access to? All that I've found is the PHB Halfling's "+1 racial bonus on attack rolls with thrown weapons and slings." bonus.
There are quite a few Halfling-exclusive bonuses for thrown weapons.
However, as far as I'm aware none are specific to throwing rocks.
- As mentioned in the question, Halflings natively get a +1 racial bonus on attack rolls with thrown weapons and slings.
- The Halfling Paragon class receives a +2 bonus on damage rolls when using a thrown weapon or a sling at 2nd level.
- The Whisperknife prestige class (Races of the Wild, p. 135) is exclusive to Halflings, and provides a wide array of bonuses to throwing attacks, including throwing-specific Rapid Shot, the ability to make throwing attacks without provoking attacks of opportunity, and the ability to flank (and therefore trigger Sneak Attacks) from range.
- The Boomerang Daze feat (Races of Eberron, p. 108) provides bonuses when throwing a specific type of boomerang, and specifically calls out that it can be selected by Halfling Fighters as a bonus feat.
- The Halfling Rogue substitution level (Races of the Wild, p. 159) provides extra Sneak Attack damage with slings and thrown weapons, in exchange for less Sneak Attack damage with melee attacks.
They are small, granting +1 on all attacks, and they have the extra bonus to throwing. That's about it. The reference is mostly because of lore from a certain fantasy series containing a completely unrelated group of little people known as hobbits. From the prologue to The Lord of the Rings:
Though slow to quarrel, and for sport killing nothing that lived, they were doughty at bay, and at need could still handle arms. They shot well with the bow, for they were keen-eyed and sure at the mark. Not only with bows and arrows. If any Hobbit stooped for a stone, it was well to get quickly under cover, as all trespassing beasts knew very well.
Note that there may be classes and feats available to halflings that further improve throwing, but a baseline halfling has only these two advantages.