The 'custom' folder contains the resources used for the main menu art in addition to the original. You can delete those you don't like to prevent them from showing up. The list below will help explain which is which.

anims_nofx.kwad
anims_nologo.kwad 
Ignore these.

gui_agentlineup - Edit of all ten basegame agents on a dark background with Incognita behind them
gui_alpha - Invisible HQ mission control room
gui_decker - Art by Cheol Joo Lee of Decker holding a pumpkin
gui_dlc - Contingency Plan box cover art
gui_incognita - Fan art of Incognita with Dr. Xu, Shalem and Prism in front of her
gui_istanbulfour - Fan edit of Derek, Rush, Draco and Olivia with the city of Istanbul in the background
gui_jet - Fan art of the agency jet in front of a city
gui_posttutorial - The agency jet from the campaign start screen
