Placeholder post; I'm currently paring down a too-large list. I'll try updating in an hour. Thanks.
EDIT: Took a bit longer than I expected, but I think I'm happy with this list. I stuck to one track per game to keep it more diverse, but ultimately a lot of my quirkier picks got jettisoned. Ah well.
RE-EDIT: Made some last-minute changes. I'm done now, I promise.
Top 5
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Castlevania: Symphony of the Night, Requiem for the Gods, http://www.youtube.com/watch?v=DBjFZq7T0W8
Final Fantasy VII, Main Theme of Final Fantasy VII, http://www.youtube.com/watch?v=6UARM4q7hHU
Legend of Mana, Song of Mana ~ Ending Theme, http://www.youtube.com/watch?v=NXSuAPqmSbo
Mega Man 2, Airman Stage, http://www.youtube.com/watch?v=FINefcN9pPc
Metal Gear Solid 2: Sons of Liberty, Main Theme, http://www.youtube.com/watch?v=Ag-O4VfJx6U
The Rest
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Adventures of Bayou Billy, Stage 1, http://www.youtube.com/watch?v=2DDQpKNBU_s
Blazblue: Calamitytrigger, Catus Carnival, http://www.youtube.com/watch?v=ig9CKXtBims
Breath of Fire IV, Breath of Fire IV -Opening Animation-, http://www.youtube.com/watch?v=-P0T8ACxq3o
Castlevania X68000, Thrashard in the Cave, http://www.youtube.com/watch?v=LZ9zNhBCVxk
Castlevania II: Simon's Quest, The Silence of Daylight, http://www.youtube.com/watch?v=H58lhgcc-nk
Castlevania: Lament of Innocence, Stone King Golem, http://www.youtube.com/watch?v=111lR--25xQ
Castlevania: Order of Ecclesia, Sorrow's Distortion, http://www.youtube.com/watch?v=WIPQTG2gcnw
Chrono Trigger, Tyrano Lair, http://www.youtube.com/watch?v=reOJi31i9JM
Command & Conquer, Just Do It Up, http://www.youtube.com/watch?v=gFNDJYU-qUs
Contra, Waterfall, http://www.youtube.com/watch?v=U58a-svZok8
Contra III: The Alien Wars, Neo Kobe Steel Factory, http://www.youtube.com/watch?v=_qjnTfCJqqw
Contra: Shattered Soldier, Intestines [Complete Version], http://www.youtube.com/watch?v=xw7PAyHDl5E
Donkey Kong Country, Fear Factory, http://www.youtube.com/watch?v=v18pEFQb3EM
Donkey Kong Country 2: Diddy's Kong Quest, Hot-Head Bop, http://www.youtube.com/watch?v=jlFYSIyAGmA
DuckTales, The Moon, http://www.youtube.com/watch?v=G_80PQ543rM
Earthworm Jim, Buttville ~ The Queen's Lair, http://www.youtube.com/watch?v=jTeMxLz_0xg
Einhander, Madness, http://www.youtube.com/watch?v=fakKuXyp470
Final Fantasy VIII, The Extreme, http://www.youtube.com/watch?v=RVkcmx2l3WA
Final Fantasy IX, Jesters of the Moon, http://www.youtube.com/watch?v=bxmgjddikwk
Gitaroo-Man, The Legendary Theme ~ Album Version, http://www.youtube.com/watch?v=4Wiu8nWMb04
God Hand, Devil May Sly, http://www.youtube.com/watch?v=LV5lqJdak2I
Grandia II, The Sairam Kingdom ~ Prosperity and Freedom, http://www.youtube.com/watch?v=P4P_aJoUAw0
Gremlins 2: The New Batch, Ventilation Shafts, http://www.youtube.com/watch?v=cEYiOviSWx4
Guilty Gear X, Calm Passion, http://www.youtube.com/watch?v=oRJU_OBwAT8
Illusion of Gaia, Around the World ~ Staff Roll, http://www.youtube.com/watch?v=MKKeT7Drc1c
Jumping Flash!, Distant Cosmos, http://www.youtube.com/watch?v=EWImnh5kV_I
Jurassic Park (SNES), Mountain Range, http://www.youtube.com/watch?v=g1EGNaPTACc
killer7, Tecks Mecks, http://www.youtube.com/watch?v=h4rMx_YnKkA
King of Fighters 2000, Inner Shade, http://www.youtube.com/watch?v=2fQyBgGf4og
Kirby's Adventure, Butter Building, http://www.youtube.com/watch?v=ronIL1A5f80
Kirby Super Star, Milky Way Wishes Staff Roll, http://www.youtube.com/watch?v=Nj6pkTO9AEA
Klonoa: Door to Phantomile, Count Three, http://www.youtube.com/watch?v=CBpwVOihivk
Klonoa 2: Lunatea's Veil, Volkies' Song, http://www.youtube.com/watch?v=cneMP38E-Vg
Legend of Zelda: A Link to the Past, Hyrule Castle, http://www.youtube.com/watch?v=BEo7UG7vnVU
Legend of Zelda: Wind Waker, Molgera, http://www.youtube.com/watch?v=5CYQzPHpvU8
Lost Vikings, Factory Beat, http://www.youtube.com/watch?v=qjUPGEQIIfQ
Lufia and the Fortress of Doom, Last Duel, http://www.youtube.com/watch?v=GzBsFGh6zoc
Lufia II: Rise of the Sinistrals, Battle 3, http://www.youtube.com/watch?v=Q7qogLxTD3Q
Mana Khemia, Nefertiti, http://www.youtube.com/watch?v=DPO2XhA5F3Q
Maniac Mansion, Michael's Theme, http://www.youtube.com/watch?v=zfgyTAvwhdg
Mega Man 5, Darkman Stage, http://www.youtube.com/watch?v=_ipPeVc0i7I
Mega Man 7, Shademan Stage, http://www.youtube.com/watch?v=ZsgbnG7ZJ4g
Mega Man 10, Against the Pressure, http://www.youtube.com/watch?v=MJR7eLyj8rY
Mega Man X, Storm Eagle Stage, http://www.youtube.com/watch?v=sayGb0MMS_k
Mega Man X4, Magma Dragoon Stage, http://www.youtube.com/watch?v=IHuzsD0Z3Qs
Mega Man X5, Burn Dinorex Stage, http://www.youtube.com/watch?v=s4qFY1b_d2U
Mega Man X8, Vs 8Boss, http://www.youtube.com/watch?v=-ypnDBa-OrY
Mega Man Zero 2, Departure, http://www.youtube.com/watch?v=PxbEoUAqtAs
Metal Gear 2: Solid Snake, Theme of Solid Snake, http://www.youtube.com/watch?v=Y0OkwTNX8aA
Metal Gear Solid, Mantis' Hymn, http://www.youtube.com/watch?v=eMasLUmBzkc
Metal Slug 4, Let's Run Through, http://www.youtube.com/watch?v=HaQSOcBEje8
Metal Slug 5, Windy Day, http://www.youtube.com/watch?v=8dKo5fjh4pU
Musashi Samurai Legend, Firewalker, http://www.youtube.com/watch?v=ras23QFu6TE
NieR, Shadowlord, http://www.youtube.com/watch?v=MGtnBnmJ8MA
NiGHTS: Journey of Dreams, Sweeping Seashore, http://www.youtube.com/watch?v=T4xWRzvfH2A
Ninja Gaiden II: The Dark Sword of Chaos, Chaosium Sword, http://www.youtube.com/watch?v=v-h3QCB_Pig
Ninja Gaiden Shadow, Stage 1, http://www.youtube.com/watch?v=JOZqb5NDstk
No More Heroes, Pleather for Breakfast, http://www.youtube.com/watch?v=DkTYXF0_d-w
No More Heroes 2: Desperate Struggle, Ms. Teller, http://www.youtube.com/watch?v=P76Nw4XH19I
Paper Mario: The Thousand-Year Door, File Menu, http://www.youtube.com/watch?v=YaxC_9Tyu8g
Parasite Eve, Urban Noise, http://www.youtube.com/watch?v=V7fhN_p1el0
Phoenix Wright Ace Attorney, The Steel Samurai, http://www.youtube.com/watch?v=YeAIC8nit5s
Plok, Main Theme, http://www.youtube.com/watch?v=xbXNfhFky70
Radiant Silvergun, Penta, http://www.youtube.com/watch?v=IdxRBDidSy8
Ratchet & Clank: Going Commando, Planet Yeedil ~ Protopet Factory, http://www.youtube.com/watch?v=7GboPS8QSCc
Ristar, Ring Rink, http://www.youtube.com/watch?v=eeViN0kt-aM
Rocket Knight Adventures, Boss Theme, http://www.youtube.com/watch?v=u0zPf6KbnrE
Romancing SaGa III, Four Noble Devils, http://www.youtube.com/watch?v=7KlXT5XQsH8
SaGa Frontier, Last Battle ~T260G~, http://www.youtube.com/watch?v=lBaoMKoABlY
Shantae, Burning Town, http://www.youtube.com/watch?v=bEp6GFqSgDY
Shantae: Risky's Revenge, She's Got Moves, http://www.youtube.com/watch?v=LjdnSKshiLQ
Silhouette Mirage, Punky Pumpkin Castle, http://www.youtube.com/watch?v=Gw8KKg9Ega0
SimCity 4, Oasis, http://www.youtube.com/watch?v=I86TfGM2OIA
Sonic CD, Metallic Madness ~ Past, http://www.youtube.com/watch?v=ZP7gYU7LL-c
Sonic the Hedgehog 2, Oil Ocean, http://www.youtube.com/watch?v=Ih8c6I1zH7I
Sonic Adventure, Bad Taste Aquarium, http://www.youtube.com/watch?v=uG-pRPxTBNo
Sonic Unleashed, Cool Edge ~ Day, http://www.youtube.com/watch?v=qa11tMeCqNE
Sonic Colors, Tropical Resort Act 1, http://www.youtube.com/watch?v=xF2KhTYb9VA
Streets of Rage 2, Good Ending, http://www.youtube.com/watch?v=Zw8KD3MmL1k
Super Mario Galaxy, Good Egg Galaxy, http://www.youtube.com/watch?v=MzYBrUl926c
Super Mario Galaxy 2, Digga-Leg's Theme, http://www.youtube.com/watch?v=urCttq22Vqc
Super Meat Boy, Betus Blues, http://www.youtube.com/watch?v=6Kf7ycHajX4
Super Robot Wars Original Generation Saga, Ash to Ash, http://www.youtube.com/watch?v=u86nGCpnp5E
Teenage Mutant Ninja Turtles IV: Turtles in Time, Sewer Surfin', http://www.youtube.com/watch?v=fH-lLbHbG-A
Tetris Attack, Lip's Theme, http://www.youtube.com/watch?v=1JUVSPpO9ZE
Tobal No. 1, Hills of Jugon, http://www.youtube.com/watch?v=fiDn6impOYw
Treasure of the Rudras, The Spirit Chaser, http://www.youtube.com/watch?v=XnW5Lkfrmrw
Viewtiful Joe 2, Ice Edge, http://www.youtube.com/watch?v=LDb3YzR4B4M
Wild Arms, Into the Wilderness, http://www.youtube.com/watch?v=gRV_A5ZDXyo
Wild Arms 3, Blood Tears and the Dried-Up Wasteland, http://www.youtube.com/watch?v=mgzsMrgSCsQ
Xenoblade, Those Who Bear Their Name, http://www.youtube.com/watch?v=V4vCEHpv6Hg
Xenogears, Solaris Eden of Heaven, http://www.youtube.com/watch?v=qH8MFPIvFpU
Xenosaga Episode 3, godsibb, http://www.youtube.com/watch?v=5krINDGIeqw
Ys 6, Quatera Woods, http://www.youtube.com/watch?v=sA_8Y30Lk2Q
Ys 7, Vacant Interference, http://www.youtube.com/watch?v=yICmlXlqKLM