You can do invisibility potion, and paralysis, fear and frenzy poisons. But not calm.
It is true- you can make paralysis potions- but the spell version works against many more creatures that will auto resist any paralysis poison.
You can make invisibility potions- but you have a limited supply and so cannot use invisibility liberaly as if you could cast it at will.
Alchemy can stand in for these two items, but it is a poor-mans version.
That is not to say that alchemy should be disregarded in these areas- i would recommend carrying paralysis poisons and a couple invis potions on hand in case you do not have the magic on hand to cast, alchemy can backup and supplement the spells- or if you cant cast the spells, it can function as a lesser stand-in.