In "Samuel was with Susan and I." Susan and I is the object of the verb. As such, standard English requires you to use me.
The NOAD has a note about using personal pronouns.
The correct use of personal pronouns is one of the most debated topics of English usage. I, we, they, he, and she are subjective personal pronouns, which means they are used as the subject of the sentence, often coming before the verb ("she lives in Paris"; "we are leaving"). Me, us, them, him, and her, on the other hand, are objective personal pronouns, which means that they are used as the object (i.e., they receive the action) of a verb or preposition ("John likes me"; "his father left him"; "I did it for her"). This explains why it is not correct to say "John and me went to the mall": The personal pronoun is in subject position, so it must be I, not me. Using the pronoun alone makes the incorrect use obvious: "Me went to the mall" is clearly not acceptable. This analysis also explains why it is not correct to say "he came with you and I": the personal pronoun is governed by a preposition ( with) and is therefore objective, so it must be me, not I. Again, a simple test for correctness is to use the pronoun alone: "He came with I" is clearly not acceptable.
As for the order of the objects, the preferred order is "Susan and me" but there isn't a grammar rule for that.