The holy water is usable. If you have alchemy level 4, you can make permanent potions with the holy water and the nescesary plants.
To use the charms, you need to find a item (normally weapon or armour), that has a "charm quality" when you have the item equiped (wearing it), you can click on it, and a little box will open with round spaces in it (equal to the charm value), take a charm and drag it into the spaces (they look crossed off, but they accept the charms regardless).
Note: you cannot take charms out ever again....
If you want more info on the charms and how to use them....
Desdemona's page of wonders is a very useful site to see what charms do WHAT exactly.
The normal gemstones (the ones you cant sell at the moment) will convert to the sellable type when you change act.... they just useful for spare cash.
The metal Rod you can chuck away (you needed it to block the gear in the prison arena).
I am not sure about the alchemy material.... so far i havnt discovered how to use it (yet) and i am busy with my 5th time in the game.