Oddly, I couldn't find it, so maybe I'm using inaccurate nomenclature, but how can I specify metadata in a recipe for items that have subitems? Like, for example, if I want to specify that my recipe uses red dye instead of just any kind of dye? Does it work the same for multiblocks?

The 3rd parameter when creating an itemstack is always the metadata. See Below:

 

ModLoader.addShapelessRecipe(new ItemStack(TFCItems.SinglePlank, 3, 0), new Object[] {new ItemStack(TFCItems.Logs, 1, -1)});

 

In the Above example notice the logs itemstack has a -1. This means that the recipe can use a log of any metadata at all. Then look at the SinglePlank itemstack, the 0 says that the result will be SinglePlank:0. I probably overexplained, but there you go. I hope that helps.