Holy crap the weapon refinery is going to shift the meta. I’ll try to list as many as I’ve found, and hopefully people can fill in the rest. (Note: I’m going with the units I have. I don’t have all the units that got upgrades.)
All upgraded staves have a choice between Dazzling or Wrathful Staff’s effect.
Gravity+ affects the target and all foes adjacent to the target.
Pain+ deals it’s effect (10 post-combat damage) to it’s target and all foes in a 2 square radius.
Fear+ gives an ATK -7 effect to the target and all foes in a 2 square radius.
Absorb+ gives 7 HP heal to all Allies withing 2 spaces of target.
The effects of the heal abilities are also changed, but they aren’t in the refinery. I’ll put them in a different post.
Fujin Yumi allows Takumi to walk through forests when HP is greater than 50%, as well as ability to warp to any Ally when above 50%.
All daggers debuff their target and any foes in a 2 square radius.
Deathly Dagger deals 10 post combat damage to target and foes in the 2 square radius, as well as preventing town users from countering.
Smoke Dagger deals a -6 debuff to all stats. (HOLY OP)
Rogue Dagger applies Def/Res debuff/buff of +/- 6 to foes/allies, with the buff affecting all allies in a 2 square radius.
Mystletainn gains Fury 3 in addition to its original effect.
Sol Katti gains Desperation 3 and Brash Assault 3, except the threshold is at 75% instead of 50%.
Zanbato negates horse buffs, in addition to its original effects.
All swords that had an upgraded form (Tyrfing, Durandal, Killing+) now have the upgraded form. So Durandal becomes Blazing Durandal, etc.
Hauteclere has the Wo Dao’s effect (+10 atk on special).
Legion’s Axe applies it’s effect on the target + the 2 square radius.
Siegmund gains Hone Atk 3 with a threshold of 90% and above HP.
Ridersbane negates horse buffs.
Naga, Excalibur, and Aura upgrade to their superior counterpart (Dark versions + Divine Naga).
Keen Wolf tomes have 12 MT and can negate horse buffs.
All breaths target the weaker stat between Def and Res.
Dark Breath’s debuff reaches -7 Atk/Speed, and can trigger on any combat.
Lightning Breath just has better MT, plus the stat targeting.
Light Breath buffs all allies within a 2 square radius Atk/Speed/Def/Res +5 after any combat.
It looks like the stat targeting is only against ranged units, but I’m not sure.
The last weapons that I know got upgraded are the spring weapons that granted +4 HP heals. They now activate on any combat.
Again,I now this isn’t every weapon that got upgraded, but these are the ones I know about. Feel free to add more!