Believe me, I know how hard it is to type the URLs on the 902! That's why I wrote the code to save the last URL and output file name in the config file. Every bit less typing helps.
This is an interesting idea. The simplest way to do this is probably to write a shell script to download the URL source file first from a fixed location, then read that file and run pbdownload.app for each pair of URL/output file inside it. It should be pretty easy to do, but I won't have time to work on it until the weekend. Does that sound like it would do what you want, or do you want to be able to input the name of the URL source file every time?