All games are PAL.
Metal Gear Solid: The Twin Snakes on GC, currently on amazon for £44.99 cheapest.
The Legend of Zelda: Wind Waker with the bonus disc that had The Legend of Zelda: Ocarina of Time and The Legend of Zelda: Ocarina of Time: Master Quest on it. Don't think it is rare but it is a personal favourite of mine.
Mario Kart: Double Dash with the Legend of Zelda Limited Edition disc that contained Zelda 1, 2, OoT and MM on one GC disc.
Metal Gear Solid on the Gameboy Colour, I had this then part-exed it (only time I have ever part exed a game) for Super Mario Advance. Years later I went to a completely different game shop and bought it for cheaper than I per-exed it for, got it home and looked at the notes in the instructions and it was my old game. Quality.
Perfect Dark on the GBC.
Bioshock on Xbox 360 Limited Edition with the Big Daddy Figurine completely intact, which I am told is pretty rare.
Psychonauts on the PS2, Beyond Good and Evil on the GC and Shadow of the Colossus on the PS2 are not that well known but are also not that rare.
Castlevania: Harmony of Dissonance and Castlevania: Circle of the Moon on the GBA are both pretty rare PAL.
And Konami Krazy Racers which is also a ludicrously rare title in the condition it is in on the GBA for PAL.
I have not even included my SNES games because they are up in the loft and I cannot be bothered to go and get them, but I remember (unless my brother got rid of them) Flashback, complete, a classic, Rise of the Robots, again complete. Jelly Boy complete (worth a decent amount) and a veritable shedload of other GB/GBC games too. Like Megaman III complete and LoZ: Oracle of Ages complete, but I have bored you enough already.