I am searching for a software that will allow me to reduce the number of colors for PNG-24 transparent (as in photoshop) files. Photoshop doesn't allow me any control over the amount of colors the PNG is saved, having this kind of software/plugin would be great.
There are two tools:
pngquant which creates 256-color PNGs with alpha channel. That greatly reduces file sizes (60-70%). In latest versions it may have better quality and smaller file size than Photoshop's Save For Web (even for images without alpha).
mediancut posterizer reduces number of unique colors in 24/32-bit PNG files. This can reduce file sizes by 20-30%, and again is smarter than posterizing colors in Photoshop as it also posterizes alpha channel and is smarter about selecting posterization levels.
Both of those programs have a GUI: ImageAlpha.
You could use ImageMagick's convert application with the -color flag.
convert something.png -color 256