wen is the accusative case. You would use it when you are asking for the direct object -- the answer will be something like "me" or "him". For example, Wen hast du gesehen? "Whom did you see?"
But since the answer here is "he", you're asking for the subject, as in "Who saw the man?" *Wer hat den Mann gesehen?"
Are you Greek? Then wen/wer is like ποιον/ποιος: Ποιον είδες; Ποιος είδε τον άντρα;
I feel like there might be a mnemonic devise here. You can think of the nominative "wer" as being similar to the nominative "er," just with a w added to make all question-sounding. Similarly, "when" sounds a little like "ihn," if you use your imagination. That's how I remember it at least.