I'm using photoshop too - had my share of "extra colors" but I've got it under control.
Some tips from me:
First of all, if you're using a graphics tablet, make sure you don't have any pen pressure settings adjusting the opacity of the brush etc. Also be sure to use the pencil tool (and pencil/block mode of the eraser tool) - those don't produce any anti aliasing. Remember to turn off anti aliasing for the selection tools like lasso/polygonal lasso, too.
Watch out for layers - it's easy to replace a color on a single layer instead of the whole picture by mistake - extra color.
Also, if you're using masks, make sure that they are strictly 0/1 - either fully white (255/255/255/) or black (0/0/0). Accidental transparencies were most often the cause of unnecessary colors in my workflow.
To keep track of your colors and keep them uniform over the whole piece, you can use the extra space of your artwork to place the blotches of the colors to work as your palette or use the swatch window.
As a means of cleaning up the color, you can use the forced color in the index color conversion dialog ( forced -> custom ) and just select only the colors you want to use (the palette mentioned above helps, since you can use the eyedropper)
As far as your artwork:
I like your shading and color choices, looks like you know what you're doing
I recommend you read up more on pixel-specific - alternatives to black outlines, manual AA and cleaning up lines - it's great you've cleaned up you're lines, but they're very angular in some places which isn't always desired - practice cleaning up some oval/curved lines for example.
The mushrooms in the tileset could use some shadow (they blend in a bit). Besides that, there's something weird going on - not sure if that's intentional, but it looks like the tileset was scaled up from a smaller size and cleaned up, but it's still kinda blocky - mainly the grass and bush tile give off this vibe.