To make quick three-color images, you can use Spot or Leopard. Go up to the "Images" menu. Pick "FITS image from disk" if you already have the images on your local disk, or the survey of your choice from the menu. Select "make this a 3-color image." Pick the color (red/green/blue) that you want that layer to be. Then, when the image loads, from the right hand side of the image window, click on "Add Color" for the next color you want, and load the data from the internet or your local disk for each of the layers. To change the stretch and/or the range of values displayed in any loaded image, click on the little box on the right of the image window that looks vaguely like a Rubik's Cube to change the stretch and the range of numbers displayed.
You can also use ds9 to make three color images. To load a 3-color image, FIRST click on Frame, then "new rgb", then you will get a pop-up window with the red/green/blue layers indicated. Pick the color you want to load. Then choose file/open and load the image. To load another layer, pick another color to load, and then file/open again. You will have to adjust the stretch. To change this, click on Scale, then "hist equ" (try other stretches too). You can also zoom in or out. "Align WCS" under "Zoom" puts north up. Drag the blue box around in the zoomed out view at the top to change what you see in the main window. If you do not like the color table, try "Color" and select one of the options there.
For more professional looking images, your best bet may be Adobe Photoshop. You should download and install the FITS Liberator plug-in for Photoshop. It helps you to handle FITS images. You should experiment with different stretches, such as the linear stretch, and the ArcSinh(x) stretch function when reading files into the Photoshop with the FITS Liberator. You can play with the layers, for example use the Color Fill Adjustment Layer with the Layer Blend set to Multiply to colorize the data or apply the Hue/Saturation Adjustment Layers with a Layer Blend of Normal. More hints are contained in an article from our sister telescope, HST.