Here are my Top 5:
5. Legend of Dragoon - If You Still Believe
4. Max Payne 2 - Late Goodbye
3. Prince of Persia - Time Only Knows
2. Tenchu - Ending Theme (Faraway)
1. Metal Gear Solid - The Best Is Yet To Come
Download all 5 here, in a convenient zip file. The Prince of Persia song is in MPC format. Here's the Winamp plugin for it. Unfortunately, it is also the shorted version from the official OST

Runner ups:
Xenogears - Small Two of Pieces ~Broken Shards~
Vampire: The Masquerade Bloodlines - {Lacuna Coil - Swamped}
Beyond Good & Evil - Home Theme
So you can probably see that my top 5 are all tracks with a balanced, high degree of composition & production value, with lyrical aspects. I don't think it matters if they opted to use licensed music. All that matters is that the song fits with the mood that you are experiencing, after the ending.
What are your top 5?