#1 and #2 mean the same thing: you wish the person was present now . #2 is the formally correct version; #1 is common in everyday English and is widely accepted. #3 means that you wish the person had been present at some time in the past .
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MailLo1- I wish he was here.1. My wish is this: He is here now.
2- I wish he were here.
3- I wish he had been here.