Let me copy-and-paste my top threes and why from a similar
RPG Maker Network thread, because I picked way too many there.
2000
1) Field4 -- My absolute favorite RPG Maker song. Sounds like an shonen theme song. The last bits of the tune really give a "winding roads" feel to an adventure before you.
2) Dungeon 4 -- Natural yet mysterious, it would work perfect for a waterfall cave or sunken ruins.
3) Fairy2 -- My goodness, it's so soft and sweet. Maybe a bit sorrowful? Perfect for innocent love, childhood memories, etc.
2003
1) Tavern -- Well-named! Very cozy and cosmopolitan.
2) IceCave -- Works well for something heavenly, or even the default name of a beautiful ice cave. Maybe a frozen castle?
3) Adventurers -- Jolly, whimsical tune of going on an adventure with your buddies! Great for a lighthearted game, or an opening act before things get serious.
XP
1) Town6 -- Has a rather rustic and ethnic feel, bustling and lively! Reminds me of something out of FF: Crystal Chronicles. Lovely stuff!
2) Theme4 -- A reprise of "Theme 3", it'd be perfect for a heart-string-tugging cutscene if Theme 3 is used for the game's title screen!
3) Battle2 -- Honestly, one of my all-time favorite RPG Maker battle tunes. Kinda reminds me of the battle theme from Dark Cloud 2 / Dark Chronicle. Courageous and fantastical!
VX
1) Field3 -- Warm and energetic! Great for a summertime adventure, or a magical vacation.
2) Battle5 -- As no VX song is designated as a boss tune, this'd work well for a mini boss. Gets you pumped up, but implies the enemy knows what they're doing. A tone of "they're tough, but we're tougher".
3) Dungeon1 -- Earthy but otherworldly, like Dungeon 4 from RM2k. More about the journey into the unknown than anything epic, with an eerie calm.
VX Ace (to be fair, I love most of them)
1) Theme4 -- Dreamy start, then hopeful and heroic when it drops the beat. If not for the third Honorable Mention, this would be my favorite RTP title screen tune.
2) Town2 -- Cozy after-hours tune to me, maybe some late-night shopping or a night on the town?
3) Dungeon3 -- Vibes of Super Mario World's ghost houses drip from this one's gothic tones.
Honorable Mentions
1) Mystery2 (2k/3) -- Lawl, Uematsu plagiarism.
2) Defeat2 (XP) -- For a short game over fanfare, probably my favorite from RPG Maker.
3) Opening1 (2k/3), or Theme3 (VX) -- Far as I'm concerned, this is the unofficial theme song for RPG Maker. ;3