In the case of your example "Has Ram or his friends come to school?", have would be more appropriate. The subject of the sentence is 'Ram or his friends', taken as a group - as there's more than one of them and if any of them had come to school the answer to your question would be yes.
This is also the case in the sentence "Neither Ram nor his friends have come to school" for the same reason.
For 'along with' on the other hand, "Has Ram come to school along with his friends?" would be correct - the subject is Ram, and the case in which the answer would be 'yes' is modified by the presence of his friends: if he's come alone, the answer is no.
"Ram has come to school together with his friends."
"Ram, together with his friends, has come to school."
The word 'together' could be dropped from either of these sentences without changing the meaning or grammatical form. Again, the subject of the sentence is Ram himself, and the presence of his friends is just a condition.