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Okay, as a basis of discussion, let me re-post some arguments pro R&L.

1. The Kingsguard at the Tower of Joy

The foremost duty of the Kingsguard is to protect the king and the royal family. After Rhaegar's death at the Trident and the Sack of King's Landing the last known Targaryens were Viserys and Queen Rhaella. So the duty of the Kingsguard would have been to seek them out and protect them, or?

Well, yes ... except if they would already protect a more important member of the royal family at the Tower of Joy.

Was Lyanna on her own more important than King Viserys and his mother? Hardly. At the least, the Kingsguard could have split to protect them all -- Lyanna, Viserys and Rhaella.

So, why didn't they split? Why did they fight Ned Stark as he wanted to go to his own sister? What had this to do with the oath they had sworn and they refered to when Ned asked what they were doing there -- fighting Ned and not seeking out the last Targaryens?

Why was the Lord Commander of the Kingsguard and the deadliest warrior of the realm, Arthur Dayne, at the Tower of Joy in the first place? Why wasn't Dayne with his closest friend Rhaegar on the Trident? Why didn't they protect Aerys'? What was so important to Rhaegar and them that the Kingsguards stayed, fought and died at the Tower of Joy in fullfillment of their oath to protect the king and royal family?

All these questions would be satisfactorily answered if Lyanna was bearing -- respectively had already born a child -- a child of Targaryen blood, the last surviving child of Rhaegar Targaryen.

2. Promise me, Ned

Ned is often reflecting about Lyanna's last living moments in which she made him promise her something -- something which was apparently very, very important to her. Also, Ned, at one point, reflects that he has paid a heavy price for keeping this promise.

Explanation: Lyanna wanted that Ned protects her and Rhaegar's child from harm, especially Robert's fury, and Ned had to pretend that Jon was his bastard child in order to cover the truth and bring Jon up as a Stark.

3. The Bed of Blood

Lyanna died in a bed of blood. A term which is used to describe child birth in the novels.

Further considering that Rhaegar had time enough to spend several months with her, it's hardly surprising that Lyanna became pregnant. In fact, Rhaegar's late return to King's Landing to lead the war can be attributed to the fact that he didn't want tp leave Lyanna until he was sure that she was pregnant.

4. The Winter Rose

Lyanna is directly linked to winter roses -- which are blue. We hear that she loved them. We hear that Rhaegar gave her a crown of winter roses at Harrenhal. Theon saw a vision of her with a crown of winter roses. And we hear that Lyanna held dead and black winter roses in the moments of her death.

This is significant because Dany had a vision in which the Wall is linked to a blue flower -- establishing a link between Lyanna and Jon.

There is also the tale of Bael the Bard who stole a Stark maiden and fathered a son on her. It's told the song of the winter rose, and refers to the actual flower as well as the Stark maiden. An analogy doesn't get much more obvious.

5. Lies, oaths, secrets, troubled sleep and Ned's blood

Ned reflects that he is living his lies since 14 years -- Jon's age at this point -- which still haunted his nights. Which terrible lie is Ned living that it can trouble him after 14 years? He also says that telling a lie can have honor, and that lies are told for love. Such as that Jon is his son to protect him while he is in truth Rhaegar's and Lyanna's child.

Moreover, Ned thinks that some secrets are too dangerous to be shared with anybody, even with loved ones. Such as that Jon is the son of Rhaegar Targaryen.

At one point, Ned reflects that he is a man who keeps his oaths. Hardly true if he would be an adulterer.

Finally, there are two instances in which Ned seems to imply that Jon isn't really his son. The one in which he tells Cat that Jon is of my blood and the one with Cersei in which he ommits Jon of a list of his children.

6. There Must Be One More. The Dragon Has Three Heads

Dany saw a vision in which Rhaegar announced that There must one one more. The dragon has three heads. This exclamation is apparently linked to the birth of his second child -- Aegon.

Interpretation: Rhaegar is expecting a third Targaryen, probably a third child of his own. Now, apparently, Rhaegar was incorrect about a part of his expectation, that Aegon was some foretold prince with a song of ice and fire, but it still indicates that Rhaegar -- for some reason, be it written prophecy or a true vision -- expects the birth of a third head of the dragon at this point.

But the only known and surviving Targaryens at the moment are Dany and Maester Aemon, so it would appear that another Targaryen might have to be found, perhaps even two if one doesn't think that Aemon's will become a head of the dragon.

There are still some other points which might support the theory that Jon is the child of Lyanna and Rhaegar, such as Tyrion's remark that Jon's mother hadn't left much of herself in him since he has the Stark look -- which could be GRRM being ironic because Jon actually looks like Lyanna.

There is also a lot of evidence which deals with Robert's, Lyanna's and Rhaegar's characters, which suggests that Lyanna was probably not raped by Rhaegar but a willing lover. Perhaps somebody else wants to summarize it?

Just a quick note regarding Harrenhal:

The time between Harrenhal and the sack of King's Landing was definitively longer than 12 months. Jon, however, was born in the time between the Sack and a month thereafter, according to GRRM. So, it's just not reasonable to assume that Jon could have been conceived at Harrenhal.