A Song of Ice and Fire (Released Spoilers)

Here are the ones I can remember for now.

1.) Rhaegar embezzled money from the treasury to fund the Tourney at Harrenhal and was planning on it being a council to plot his overthrow of the Mad King. Varys finds out and alerts the King, thus why he unexpectedly shows up.

2.) Elia Martell, Rhaegar's wife, is shown as a willing participant in this plot and understands that Rhaegar needs another woman to have more children with since she cannot. She says she is his political wife and is ok with him having a wife for love as well. The love of Elia's life is Ashara Dane and they were together in secret. Elia was still angry that Rhaegar crowned Lyanna at the end of the tournament because Lyanna was supposed to be a secret, not the open queen.

3.) At the Battle of the Trident, Robert is actually being beaten pretty badly by Rhaegar. Rhaegar keeps asking him to yield and tells him that he promised Lyanna not to hurt him. So Robert knows even then that Lyanna is with Rhaegar for love and does not want to be with Robert like that. The battle only ends when Rhaegar has a vision during the fighting that offers Robert an opening to kill him.

4.) Ned's promise to Lyanna (Promise me Ned) is a promise to not tell Jon a single thing about his parentage so that he can make his own choices in life. It is either stated or heavily implied that Lyanna is having wolf dreams and they get more intense when she is around Rhaegar. She was all about the Prince that was Promised prophecy (as were the Kingsguard that followed Rhaegar) until it led to everyone involved being killed for trying to pull off a grand conspiracy.

All really good stuff.