I have used a variety of thread in the garment. Different colors and thicknesses and content of thread can all be used, again depending on what you want to emphasize or be more subtle. I can't even say which I like best but here are a few I have used.
Colors: The color for each piece will vary depending on my vision for the finished item. I have some lovely lace I wanted to use to hold the cotton shirt together so I have used black thread primarily. I have also used purple because it is dark but I have used it sparingly. And, as always, I have used a variety of neutrals. I generally use the neutrals in the more simple and quicker to make stitches since the stitches will generally only be seen upon close examination.
Type of Thread: For this garment I have used cotton, silk, and wool thread. All work better if you use some bees' wax on them first. Silk is a bit hard to use but looks lovely with the silk shine. I have used it mostly for the buttonhole stitches around the lace. I love the hairiness of the wool thread. Cotton is the staple.
Thickness: Again, I wish I could give you one answer but I use one, two, three, or all six embroidery threads depending on how thick of a line that I want. I also use crochet thread and much heavier threads (see the yellow thread in the picture). So far I have not used yarn but I do want to try it on a future garment.