"Who did you speak with?" is a question on its own. It doesn't really make sense to say after "I wonder" unless you said "I'm wondering - who did you speak with?" The second option is best. "I'm wondering who you spoke with." As Marcel said, this is not technically correct. In proper English (in formal writing) say "with whom you spoke" because you can't end a sentence with a preposition (with). However, nobody actually speaks like this. Hope this helped! Let me know if you have any questions.

The answer depends on whether you use 'I wonder'. "Who did you speak with?" Is a question on its own. To use your second choice, you need the 'I wonder' - 'I wonder who you spoke with'

it is number 2

The second one would be more correct but, it would be using very casual English.

Your second is more correct, but proper English would be, « I wonder with whom you spoke. » One should not end their sentences in prepositions. What time are you leaving at? Becomes At what time are you leaving?