This documentation is currently very incomplete, but might still be helpful.
Updates to this will come whenever I work more in Project Base.
-Grime

:::::UNUSED COLORS FOR ENEMY PALETTES:::::

Enemy ID                      Palette pointer: unshared
CFBF (PUYO/yellow slime)      -> 998D [unused colors: 5, 10-16
CFFF (SABOTEN/cactus)         -> 9E6A [unused colors: none]
D03F (TOGE/sand turtles)      -> A38B ***
D27F (swooping yellow thing)  -> BA7B [unused colors: 9]
D3BF (HIRU/jump-float things) -> D80C [unused colors: 3]
D3FF (RIPPER 2)               -> E17B [unused colors: none]
D43F (red RIPPER)             -> E2C0 [unused colors: none]
D47F (ripper)                 -> E457 [unused colors: 10-13]
D67F (METAL SKREE)            -> 88F0 [unused colors: none]
D6BF (FIREFLY)                -> 8C0F [unused colors: 4]
D7FF (KAMER/platform things)  -> 9B7B [unused colors: 3, 9]
D87F (SBUG)                   -> A051 [unused colors: 9, 13-16; shared with unused SBUG]
DB7F (skree)                  -> C63E [unused colors: 10]
D6FF (FISH)                   -> 900A [unused colors: 3, 9-13]
D77F (KANI/ORANGE CRAB)       -> 965B [unused colors: 3, 4, 10-13]
D93F (SMALL SIDEHOPPER)       -> AA48 [unused colors: 6, 7, 9]
D9BF (LARGE SIDEHOPPER)       -> B085 [unused colors: 7]
DC7F (ZEELA)                  -> E23C [unused colors: 3, 6]
DCFF (zoomer)                 -> E5B0 [unused colors: 9]
E5BF (ETECOON)                -> E7FE [unused colors: 6]
E5FF (DRACORA)                -> F225 [unused colors: 9 - *MUST FIND/EDIT SHINESPARK COLORS LATER*]
E6BF (EYE)                    -> 8F8C [unused colors: none]
D0FF (MERO/crat. flies)       -> AFF3 [unused colors: 9]
DD3F (metal zoomer)           -> E5D0 [unused colors: 9]
E7BF (HAND/grabber things)    -> 8F4F [unused colors: 2, 3, 10-16; not sure if 10-16 are safe to use without overwriting other data yet]
E7FF (KAGO)                   -> AAFE [unused colors: none]
E8BF (PUU/grapple puffer)     -> C143 [unused colors: 2, 3
EA7F (KOMA/blue heads)        -> E7AC [eye/mouth glow at $1467CC-1F]
E87F (NOMI/hopping leech)     -> B65E [unused colors: 3, 9]
F193 (ZEB/red pipe flies)     -> 878B [unused colors: 16]
F1D3 (crat. mound flies)      -> 89FD [unused colors: 4]
F253 (GEEGA/pipe flies)       -> 8EDC [unused colors: 3]


Enemy ID                      Shared colors, different palette pointers (wut)
D7BF (OUMU/green/red slugs)   -> 980B [unused colors: #3
E9BF (walking lava dragons)   -> DBC7 [body palette at 11980B-0F; unused colors: #6]


Enemy ID                      Same palette pointer, unshared colors (wut)
CEBF (BOYON/hopping slime)    -> 8687 [unused colors: 10-16; not sure if safe to use]
D63F (waver)                  -> 8687 [shared with others]
F653 (crat. pirates)          -> 8687 [shared with others]

Enemy ID
D07F (Samus's ship)           -> A59E
D0BF (Samus's ship's bottom)  -> A59E

Enemy ID                      Same palette pointer, shared colors
EABF (HACHI GREEN)            -> E99A [unused colors: none]
EAFF (HACHI GREEN WINGS)      -> E99A [unused colors: none]
D4FF (SHUTTER)                -> E978 [unused colors: 2-9, 16]
D53F (SHUTTER)                -> E978 [unused colors: 2-9, 16]
D57F (SHUTTER)                -> E978 [unused colors: 2-9, 16]
D5BF (SHUTTER)                -> E978 [unused colors: 2-9, 16]



F693 (green missile pirate)  -> 86A7 [doesn't seem to be shared?]




:::::UNUSED COLORS FOR AREA TILESETS:::::
:::::ONLY SAFE TO EDIT AFTER YOU'VE REPOINTED THE PALETTE:::::

tileset #12 - unused (line #3): 61

tileset #13 - unused (line #3): 36, 37, 38, 39, 40, 41, 42, 43 (supposedly used only for the quicksand tiles, but the quicksand colors are actually stored elsewhere in the ROM - I'm a Genius offset: 213975-07)

tileset #13 - unused (line #5): 81, 82, 83
tileset #13 - unused (line #6): 110

tileset #14 - unused (line #4): 72, 77, 78, 79
tileset #14 - unused (line #5): 81, 82
tileset #14 - unused (line #6): 105, 106, 107, 108, 109, 110, 111

tileset #15 - unused (line #3) 55, 60, 61, 62