Fire Emblem Radiant Dawn.
Currently it's going for around $90 on ebay and such.

I have that one as well!

My original WoW install disks and Burning Crusade box as well (all 7 discs lol), probably my SCII and Heart of the Swarm physical copies to boot.

I realsied the past 2-3 years I've practically stopped buying physical, I do miss some physical games but at the same time I find digital a lot cheaper and easier for me to manage while still holding the odd physical disc/box or two to look back on with fond memories.

Not really sure because brand new games can go for a lot more than used games.

Unopened Smash Bros Melee goes for a lot while used could vary greatly in prices.

HMMM....
I have Castlevania 1 and 3 NES both sealed in original wrap.
The original DooM 1st episode shareware CD sealed and autographed by Romero.
I have an original copy of Strife. (last commercially made game to use the DooM engine)
Sealed and autographed copy of Tribes.
Sealed non-Greatest Hits Symphony of the Night.

Fire Emblem Radiant Dawn
Conkers Bad Fur Day N64
Ogre Battle 64
Xenoblade
Paper Mario thousand year door

Earthbound, Metroid Prime Trilogy, complete Super Metroid and soon physical edition of Retro City Rampage on Vita.

Panzer Dragoon Saga is easily the most valuable game I own (and I have quite a large collection). Copies in inferior condition to my own regularly fetch over $300 on eBay.

Xenoblade Chronicles (Special Edition)
Wario Land: Shake Dimension (at least in Spain is pretty rare)
Last Window: The Secret of Cape West
Metroid Prime Trilogy (Steelbox)

I've got a copy of Super Metroid in-box, everything looking pretty much mint.