Well, Lizardmen are nice in that it's more about your personal preference rather than a set color scheme. The painting section of the BRB gives a few suggestions for the basecoat, and I think most prefer black since it keeps the schemes darker. Most people don't tend to like the blue color scheme suggested by GW, and so you'll see quite a variety in color from person to person (the different threads in this section give a good indication of that). The only thing I can suggest is that you give the proper coloring for any sacred spawnings you put on your models. After that, it's all up to you.
If you're going for a "natural" reptilian look, go with darker greens, browns and grays.
If you want something more original, just pick a random color or two and a brighter version of them for highlights.
And if you go with the GW standard, see p. 44 of the lizardmen rulebook.