I think it'd have to have been CastleVania: A Vampires Kiss and CastleVania Legends. I used to have a complete CastleVania set but ended up selling them with 90% of my game collection over the last couple of years.

I got £297 ($480ish) for CastleVania Legends on ebay.

For what I currently have left in the collection (still being sold off as it's no longer practical to keep the full whack, so just moving onto 8th gen and hoping to get settled for a few years) I'd have to say my Ni No Kuni Limited Edition set and Samba De Amigo PAL release with European packaging Maracas are probably the most valuable ones I still have.

Probably Metroid Prime Trilogy.

It used to be Metroid Prime Trilogy, but I  probably lost that game , so my answer is Xenoblade.

For me its Dragon Quest VIII, it was a miracle that I could find it over here.

Judging from prices on amazon;
bravely default CE
tales of symphonia CE,
complete .Hack// series(kite and haseo's story)
Xenoblade
Xenosaga trilogy
God of war III CE
Tales of Xillia CE
60gb PS3
Suikoden 3-5
Crimson gem saga
Hexyz Force

Pokemon Colosseum&XD Gale of Darkness

Now most of these aren't super rare, just some that have retained/held on from their initial value

I don't know if it's worth anything, but I treasure the copy of Blade Runner I own.

I couldn't tell you which is worth the most, or which is the most rare, but I have a few:

Ys: I and II Complete Japanese PC Edition
Ys: The Oath In Felghana (Japanese PC edition, big box, around 8 or so CD soundtrack)
Batman Arkham Asylum Collector's Edition PS3
Metroid Prime Trilogy
Warcraft 3 Collector's Edition
Every World of Warcraft Collector's Edition
Every Starcraft 2 Collector's Edition
Skyrim Collector's Edition PC
Oblivion Collector's Edition PC
Borderlands 2 Loot Crate edition PC

Yeah, I'm a sucker for Collector's Editions. I imagine those two Ys games would be worth a pretty penny right now. Can't even find them on eBay at the moment.

DBZ 2 In 1 Legacy of Goku I & II for the GBA, according to VGChartz only 0.08m copies were released

probably a nintendo game & watch greenhouse

Bad Fur Day for n64 I dont even think its a rare game (value wise not the company Rare) but some how its 90$ used.

I got it a long time ago maybe 2001/2002 and never really liked it other than the multiplayer.