What I usually do is grouping the scrips by abstractions and type. Meaning, I have 1 script per transactions server side, 1 per transactions client side, 1 per entity server, 1 per entity client, 1 per custom records server etc'.
The common and shared functions go to modules.
Processes that are stand alone, such as scheduled scripts, map/reduce etc' have their own script.
Regarding the size of the script, it has importance mainly on the client scripts.