You can place a character such as '_' at the beginning of the folder names for the mods you want to appear at the top. This should cause them to appear at the beginning of the list.
Col. Mustard said:
What are the best mods keeping to the general features of the original game?
My favorite is the DevNull mod... It does a great job balacing some issues... For example, it manages to make missiles viable for a much longer period of time.