
Mysterious Stranger |

Scrolls are spell completion items so you are actually casting the spell. The book states you to cast the spell as if you prepared and cast it. Therefore you can make any decisions on how it acts that you would if you cast the spell.
Potions specifically state the maker of the potion decides how it works when the potion is created.
Wands are spell trigger items which means you are not actually casting the spell. The rule book does not specify on way or another if you can make the decision on how the spell operates. Considering the nature of some of the wands listed in the book it would seem you can control the effects of the spell. A wand of suggestion is kind of useless if you cannot control what the suggestion is.

Azothath |
RAW states that all spell parameters for items are defined. This is mainly for UMD users as some spells have things that can be tweaked or defined at casting and that, in a general way, requires Spellcraft or material components.
So with Polymorph you should define the target form, or Energy Resistance the energy type. This keeps things well defined in case the user can't or doesn't try to change the parameters.
For the specifics, as commented, review the magic item description and item creation feat.

Pizza Lord |
Like Mysterious Stranger said, potions are chosen at the time of creation. So you won't have a potion of resist energy, you'll have a potion of resist energy (fire) (as seen on the potion list). Other items like scrolls and wands are chosen at the time of casting like normal, unless there's a special case or something, like if the creator only used a certain value of opals or crushed diamonds, limiting the item to its effect.