This is kind of a complex enhancement. I'm considering trying to implement it myself, and if I do, I'll be sure to let you know. Additionally, I can get this functionality out of a few other bag addons, but I love bagnon so much that I don't want to switch.

Basically, I go farming and I get a bunch of junk. I use trashcan to delete the useless junk items that sell for next to nothing, but I also move all of the items that I'm going to sell to the bottom so it makes for easy selling when I go to a merchant.

It'd be cool if you could allocate a portion of the inventory(perhaps just select a bag), and have items that are either on a list, or meet a criteria such as sell price or item level, go to this designated area.

A simple addition to THAT is a sell these items button on that separated portion that will auto sell those items.

You could also use an addon like Scrap (http://www.curse.com/addons/wow/scrap) to get rid of the unwanted items automatically the next time you visit a vendor.

Nevertheless some "sorting options" for Bagnon would be awesome.

Sorting is already on the roadmap :D
Regarding finding the junk items, Scrap is really the best way to go - it will find them for you.