I believe there's an alternate foil cover art for Xenosaga Ep III available out there but its somewhat difficult to find.
Most Collector's/Special/Limited Editions at least have alternate box art, so I won't name too many here:
Conan, Stranglehold CE on the Xbox 360 also has shiny artwork.
Oni on the PS2 had shiny artwork as did The Matrix: Path of Neo (Enter the Matrix maybe, I have the Player's Choice version which isn't, but the original might be).
Deus Ex on the original Xbox had shiny artwork.
Battlefield: Bad Company Gold Edition has a gold slipcase and alternate box art (grenade and title on a pure white background)
Phantom Brave on the Wii has a slipcase and the Conduit SE has alternate, shiny artwork.
Fable II LE has a slipcase and alternate, double sided artwork.
Prinny: Can I Really Be the Hero for the PSP comes with a slipcase (and a soundtrack) as does Ys on the DS
Both the PS3 and standard 360 versions of Bioshock had Slipcovers
There is a version of Enchanted Arms with a slipcase and a short graphic novel. Never officially an LE.
Many, many PC games come in slipcases (I just bought Sherlock Holmes vs Jack the Ripper with a slipcase) but the game Evidence has pretty nice packaging. Its basically a dvd case labelled to look like police evidence inside a plastic evidence bag.
There are also two versions of Gran Turismo 3 on the PS2. There's the standard edition that's mostly blue then there's the one that was included in a PS3 bundle that's all red.
And that's all I can think of off the top of my head
Prey (large metal box w/ pewter figurines and artbook)
The Dark Spire (Cardboard outer box w/ soundtrack)
Dragon Quest VIII (Cardboard outer box)