If I control a Panharmonicon, I can have more cards imprinted on an artifact than was intended. For most cases, it seems that you would just select one card from the exiled cards (for example, Isochron Scepter. What if I have a Prototype Portal with a 2 drop and a 4 drop? What is the cost to activate the ability? Could I pay 2, then get a copy of the 4 drop?
Anytime a card with Imprint (or other cards that have a triggered ability that is linked to a second ability) refers to 'the exiled card' it really refers to both cards. In cases like Prototype Portal (where it looks at properties of exiled card) you would have to look at both cards, and add their CMCs together. You would then get to make tokens of both cards.
From the Gatherer rulings on Panharmonicon:
If a triggered ability is linked to a second ability, additional instances of that triggered ability are also linked to that second ability. If the second ability refers to “the exiled card,” it refers to all cards exiled by instances of the triggered ability. For example, if Isochron Scepter’s enters-the-battlefield ability triggers twice and two instant cards are exiled, both will be copied when its second ability is activated. You may cast either or both of the copies in any order.
In some cases involving linked abilities, an ability requires information about “the exiled card.” When this happens, the ability gets multiple answers. If these answers are being used to determine the value of a variable, the sum is used. For example, if Elite Arcanist’s enters-the-battlefield ability triggers twice, two cards are exiled. The value of X in the activation cost of Elite Arcanist’s other ability is the sum of the two cards’ converted mana costs. As the ability resolves, you create copies of both cards and can cast none, one, or both of the copies in any order.
Imprint abilities are a type of abilities called Linked abilities. In particular with Imprint, the second ability on the card always refers specifically to cards exiled by the first ability on the card. Rule 607.3 describes how to handle the case where more cards than expected were exiled:
If, within a pair of linked abilities, one ability refers to a single object as “the exiled card,” “a card exiled with [this card],” or a similar phrase, and the other ability has exiled multiple cards (usually because it was copied), the ability refers to each of the exiled cards. If that ability asks for any information about the exiled card, such as a characteristic or converted mana cost, it gets multiple answers. If these answers are used to determine the value of a variable, the sum of the answers is used. If that ability performs any actions on the exiled card, it performs that action on each exiled card.
This results in the following interactions:
Isochron Scepter's activated ability allows you to cast a copy of each exiled card without paying their mana costs.
Prototype Portal's activated ability has a cost equal to the sum of the converted mana costs of the exiled cards, and creates a token copy of each one.
Strata Scythe gives the creature +1/+1 for each land on the battlefield with the same name as any of the exiled cards.
Spellweaver Helix's ability triggers when a spell with the same name as any of the exiled cards is cast, and then allows you to cast a copy of each of the other exiled cards.