Non-repeatable
- Fiery Path (Southwest corner; requires Strength)
Repeatable
- Route 124 (Red Shard trade)
- Mauville City (Inverse Battle reward)
- Secret Super Training (The Fire Stone Cup Begins!, The Battle for the Best!)
- Route 114 (Kindler Bernie rematch)
- Secret Base (Pick up stones with Secret Pal)
Non-repeatable
- N/A
Repeatable
- Route 124 (Blue Shard trade)
- Mauville City (Inverse Battle reward)
- Secret Super Training (The Water Stone Cup Begins!, The Battle for the Best!)
- Route 106 (Fisherman Elliot rematch)
- Secret Base (Pick up stones with Secret Pal)
Non-repeatable
- New Mauville (Front room in the northeast)
Repeatable
- Route 124 (Yellow Shard trade)
- Mauville City (Inverse Battle reward)
- Secret Super Training (Follow Those Fleeing Goals!, The Battle for the Best!)
- Route 117 (Triathlete Dylan rematch)
- Route 118 (Guitarist Dalton rematch)
- Secret Base (Pick up stones with Secret Pal)
Non-repeatable
- Route 119 (Southern tip of the middle river; requires Surf)
Repeatable
- Route 124 (Green Shard trade)
- Mauville City (Inverse Battle reward)
- Secret Super Training (The Leaf Stone Cup Begins!, The Battle for the Best!)
- Route 118 (Aroma Lady Rose rematch)
- Secret Base (Pick up stones with Secret Pal)
Non-repeatable
- Meteor Falls (Western hill on 1F)
Repeatable
- Pickup (starting at Level 41)
- Mauville City (Inverse Battle reward)
- Secret Super Training (Drag Down Hydreigon!)
- Jagged Pass (Expert Shelby rematch)
- Secret Base (Pick up stones with Secret Pal)
- Held by wild Clefairy and Lunatone (5%)
Non-repeatable
- Mossdeep Space Center (Given by a Sailor on 1F)
Repeatable
- Pickup (starting at Level 31)
- Mauville City (Inverse Battle reward)
- Secret Super Training (Drag Down Hydreigon!)
- Route 115 (Expert Timothy rematch)
- Secret Base (Pick up stones with Secret Pal)
- Held by wild Solrock (5%)
Non-repeatable
- Route 121 (The area with flowers; requires Cut)
Repeatable
- Mauville City (Inverse Battle reward)
- Secret Super Training (An Opening of Lighting-Quick Attacks!)
- Mt. Pyre (Fairy Tale Girl Momo rematch)
- Secret Base (Pick up stones with Secret Pal)
Non-repeatable
- N/A
Repeatable
- Mauville City (Inverse Battle reward)
- Secret Super Training (Watch Out! That's One Tricky Second Half!)
- Mt. Pyre (Hex Girl Valerie rematch)
- Secret Base (Pick up stones with Secret Pal)
Non-repeatable
- Victory Road (Given by Wally after the battle); requires Surf and Strength
Repeatable
- Mauville City (Inverse Battle reward)
- Secret Super Training (Those Long Shots Are No Long Shot!)
- Sea Mauville (Mysterious Sisters Scall & Ion rematch)
- Secret Base (Pick up stones with Secret Pal)
Relevant links for some of the more complex game mechanics:
Secret Super Training (Bulbapedia)
Secret Bases (Bulbapedia)
Inverse Battle Stop (Bulbapedia)
Inver (Bulbapedia)