Looks like a good start. I think it's better to take maybe half this number of colours and just start redrawing/recolouring the sprites. If you find you need a new colour then just add it. So try using some of what you have and see how it goes. Complimentary colours are your friend :)

Hey thanks for for replying. I am using the "pick and choose later" method now and it is helping. I wanted each level in the game to have a certain color theme and I guess I got too ahead of myself with planning.
Here's some assets on a level of a abandoned circus.

Thanks again!

Those are looking really great. A few things:

1) They are overall quite dark and low contrast. Is this intentional for their context in-game?

2) Perspective. Is this supposed to be an isometric type view or should there be some perspective on the stall? In my opinion you could add a bit of perspective (2 vanishing points) if you aren't restrained to an isometric grid (from your original game screenshots you definitely don't seem to be).

3) Number two kind of begs the question of depth. How are you going to represent depth in-game? The character on the left is very flat, and the stall is three dimensional with some shadows to boot.

4) Pick and choose later - good choice especially if you have software that supports adjustable indexed palettes. Just watch your values as per number 1 - right now they are all similar brightness but different shades. You would probably do better to focus on black and white then pick the colours later.

hehe...that just means you want a 'green' so you use the first green you have and then optimize and tweak later on when you have other colors also chosen in the 'pick and chose later' way so that the time you spend in color optimizing and unification is limited not too mention that the ending 'green' may not even be green at all.

To respond to rociflier:
1. Yes its supposed to be dark as it's set at night time. Plus there will be lights in the game which brighten it quite a bit.
2. It's isometric. For this particular use of the tent it needs to be isometric.
3. The character on the left is a card board cut-out so there is not a lot of depth but I will see what I can do. It's true it does look quite.. flat.
4. I've tried black and white but its very hard for me to draw if I don't have the "moods" of the color to help me set the tone.

ah. well. i tried. ha