Off the top of my head I also have:
DBZ: Tenkaichi 3 (Wii)
Mario Kart 64 (N64)
Zelda Wind Waker (GC)
Zelda Four Swords Adventures (GC)

I have a sealed bigbox of the original Carmageddon for PC, found it on ebay for cheap and couldn't resist. I had planned on opening it on the end of the world (21/12/2012?) but was too lazy.

Burning Rangers!!! Man I would LOVE to see a remake of that now that 3D hardware is powerful enough to run it properly.

Still gutted the Dreamcast never saw a sequel.

A brand new copy of "Grandia", my pride and joy. Xenoblade would be the runner up.

Forgot I have the 5th anniversary edition of Oblivion for PS3. Seems like that will go up in value over time as it was a limited release.

Xenoblade complete with its artbook as well as Shadow Hearts, though the manual is a little roughed up.

Probably this one, in terms of rarity at least:

I had a complete copy of Xenoblade and Metroid II:The Return of Samus which is rare according to crazyman lol.

Money value:
Skies of Arcadia - Dreamcast PAL
quite expensive

Skies of Arcadia Collector's Edition - Dreamcast Japan
quite rare

Samba De Amigo Box - Dreamcast PAL
rare and expensive
http://www.ebay.de/itm/Dreamcast-Samba-de-Amigo-inkl-Maracas-Matte-mit-OVP-Big-Box-US-NEUWER-/290901943093?pt=PC_Viedeospielzubehör&hash=item43bb1b6335
^and that is NTSC which isn't that rare

Personal value:
Ikaruga - Dreamcast Japan
still sealed

Donkey Kong Jr Math on NES (complete in box). Last time I checked on Ebay someone was trying to sell it for $100,000. hahah no shit!!