Sorry if I forget something, but here is what comes to my mind atm...

Save up for rebates or other purpose:
- Seal scrolls
- Summon scrolls
- Charm material
- Refinement runes
- Mysterious cave keys
- Battle Armor threads
- Coupons (use when you can do a full Fukurokumaru deal event)
- Skill Breakthrough material (wait for some ninja you really want to get fully BT, dont waste it)

Do not save up (no rebates / no need to save up):
- Moon / Sun scrolls + mysterious stones
- Training potions
- Secret scroll pages and elixirs
- Mount Myoboku material
- Purification material
- Ninja assist link material (Chimes and bond scrolls)
- Battle Armor cloths
- Eight gates training points
- Treasured tools material and scrolls
- Magatamas
- Runes
- Mood scrolls
- Awakening material
- Equipment upgrade material
- Purification breakthrough pills
- Those Nature chakra training scrolls (not sure what they are really called...)

That´s all I can think of right now... maybe someone will add something whats missing xD