FunkMaster, Culex Battle from SMRPG is the same as FF4 Boss Battle, it's a nice song cameo
8000, those links don't work for me, but it's nice to see there are other people who enjoyed Radiata Stories.
Mega Man Series:
2: Main theme, Bubbleman, Flashman, Crashman, Airman, Dr. Wily Stage 1
3: Title (I just started playing it >_>)
X: Opening Stage, Spark Mandrill, Storm Eagle, Boomer Kuwanger, Sigma Stage 1, vs. Sigma
X2: Opening Stage, Bubble Crab
X3: Opening Stage, Blast Hornet, Crush Crawfish, Toxic Seahorse, Gravity Beetle, Vile, Zero's Theme
X4: Colonel
X5: Main Theme, Dynamo, X vs. Zero, Sigma Stage 2, Duff McWhalen, Grizzly Slash, Squid Adler
Chrono Trigger/Cross: EVERYTHING
Sonic:
1: Green Hill Zone
3&K: Flying Battery Zone, Ice Cap Zone, Doomsday Zone
Final Fantasy:
I: Battle Theme
IV: Battle, Boss Battle, Dreaded Fight, Zeromus
V: Battle With Gilgamesh/Clash on the Big Bridge
VI: Dancing Mad, Decisive Battle
VII: Aeris' Theme, Boss Battle, J-E-N-O-V-A
VIII: Man With the Machine Gun, Don't Be Afraid, Force Your Way
IX: Vamo 'alla Flamenco, Battle, Hunter's Chance
X: To Zanarkand, Blitz Off, Battle, Otherworld, Seymour Battle
XII: Battle With Gilgamesh/Clash on the Big Bridge
Starfox:
SNES: Corneria
Guilty Gear:
X: No Mercy, Holy Orders, Awe of She
XX: Noontide, Holy Orders, Awe of She
Secret of Mana:
Main theme, Meridian Dance
Earthbound:
Giygas & Pokey
Street Fighter 2:
Ken Stage, Guile Stage, Cammy Stage, Ryu Stage
Lufia 2:
Battle, Boss Battle, Sinistral theme
I'm probably missing a million others <_<