Paul McCartney said that he wrote the song for John Lennon's son Julian. John abandoned the five-year old and his mother, Cynthia, when Yoko Ono entered the picture. And McCartney, knowing that things were hard for John's former wife and son, decided to pay a visit. On the way there, he wrote a little song intended to cheer up the young Julian: "Hey Jules, don't make it bad, Take a sad song and make it better." He later changed it for "Hey Jude" because it sounded better.

The obvious meaning of the song is that he's giving advice about how to conquer a girl, but considering the original inspiration as confessed by Paul McCartney (to bring comfort to a 5-year-old boy), the girl-stuff is out, and that "her" he talks about is probably a personification of the sad song he is talking about, and once again, the sad song is a metaphor for the painful situation the little boy was going through. Or... it's a reference to Yoko Ono, his nes "mum".

In 1987 Julian ran into Paul in New York City when they were staying at the same hotel and he finally heard Paul tell him the story of the song firsthand. He admitted to Paul that growing up, he'd always felt closer to him than to his own father. In Steve Turner's book The Stories Behind Every Beatles Song, Julian said: "Paul told me he'd been thinking about my circumstances, about what I was going through and what I'd have to go through. Paul and I used to hang out quite a bit - more than Dad and I did... There seem to be far more pictures of me and Paul playing at that age than me and Dad. I've never really wanted to know the truth of how Dad was and how he was with me. There was some very negative stuff - like when he said that I'd come out of a whisky bottle on a Saturday night. That's tough to deal with. You think, where's the love in that? It surprises me whenever I hear the song. It's strange to think someone has written a song about you. It still touches me."

When McCartney played this song for John Lennon and Yoko Ono, John interpreted it as being about him; he heard the line "You were made to go out and get her" as Paul imploring him to leave his first wife and go after Yoko ("I always heard it as a song to me," said Lennon). This was one of Lennon's more narcissistic moments, as he failed to grasp that the song was written for his son.

This is a possible interpretation of the meaning of these lyrics:

Alright. Well first off, this song was written for julian lennon during John and cynthia's divorce. Definitely not heroine.
"hey jude, don't make it bad"-don't make the seperation harder than it has to be.
"remember to let her into your heart, then you can start to make it better"-accept yoko, you may start to feel better.
"and any time you feel the pain, hey, jude, refrain
don't carry the world upon your shoulders"-possibly not to put the pressure onto yourself, the divorce isn't your fault.
"so let it out and let it in, hey, jude, begin
you're waiting for someone to perform with.
And don't you know that it's just you, hey, jude.
You'll do, the movement you need is on your shoulder"-let your feelings out, and try to welcome yoko.
You think someone is going to speak for you, but it's you that needs to make the decision to accept her...

Anyway, just what I think.