For me it would be:

• Dreamy Pilot (unused stage 4 theme for LLS) - I kinda understand why ZUN removed it (it's not stage 4 theme-y enough IMO, this theme pales in comparison to Alice Maestra which got used), and it's a bit too repetitive, but it's such a too good track to be left scrapped... JynX's remix showed that it can sound like a boss theme too.
• Sunfall (unused stage 2 theme for SoEW) - This theme reminds me of HRtP, it would've been perfectly fine there I feel. But yeah, by current standards it's kinda bad (there's very little progression), but there's some really good potential here.
• Winds of Time (unused theme for PoDD) - This is another theme that is too good to be left scrapped. Too bad this theme doesn't fit with any character in the game (contrary to popular belief this doesn't belong to Chiyuri, it was only a test theme during the game's development)... Funny that ZUN quickly created a character for the theme Vanishing Dream ~ Lost Dream when he realized it wouldn't work well for Yumemi who's going to be the final boss, but not this theme...
• Shrine of the Wind (unused track from HRtP) - Not only is it unused, it was never even remixed for Mystic Square's Music Room nor remastered for Akyu's Untouched Score. Completely forgotten, even worse than Mima's situation! I think such an upbeat track like this could be used in one of the fighting game spinoffs...