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What all types of siege weapons could an Alchemist come up with OR improve upon? HAVE SOME FUN ON THIS ONE!!!

Plenty of magical "pots" for a catapult. Lob a nice magical slumber pot over a wall, or carpet of adhesion pot. Maybe a fireball pot?

Magical flaming arrows for a ballista instead of using mundane ammunition. A fireball cannon.

A rat-stone; primarily used for catapults, the rat-stone is in fact a swarm of rats that have been transformed into a single catapult stone. The rat-stone stays solid indefinitely until it is fired. A few seconds after impact, the stone's hold is released and it tranforms into the the swarm of rats. This can be used for 3 reasons, the first being the unsettling effect of a swarm of rats overruning entrenched castles (the shock factor associatd with rats) . The second being to infest a castle with verim, that will impact and dimished the siegee's food stores. The thrird and insidious, is, if plagued rats are used at the time of transformation, to introduce various plagues to the people under siege, thus again reducing the seige time for the attackers.

I'd say that one could make any siege weapon easier to transport.

I'd mostly set the alchemical siege weapons to be for psychological warfare.
Stones that release a fog of fear or some such to cause incalculable panic behind the walls. Perfect for launching just before the besieging army makes an attempt to break over the walls.
Alternatively one could have a stone to flesh. Defenders would seriously have problems if the enemy were launching lumps of flesh at them.
In all honesty though, unless its to increase the damage output of the war machine then the efforts would be quite likely best spent elsewhere, especially because I'd imagine it would cost a lot of money to get the alchemical enchantments done.

Or you can reverse that and get a toy catapult that when a command word is given, grows into a normal sized catapult.

A fast firing weapons.

A battering ram that is impervious to fire and casts the earthquake spell when it impacts a solid object would be nasty.

a battering ram that has Featherlight and Increase Weight enchantments, feather weight when pulling it back, increase weight when battering forward, also anyone touching it is immune to fire.