CUSTOM is better than GX. GX is slightly better than SOFT.
The rule: Top is better than bottom
CUSTOM are settings files made by scene devs to fix issues. Most of them were created by kozarovv, mrjaredbeta or agrippa.
NET are settings files included in PS2 Classics found on PSN Store. If there are CUSTOM they make improvements.
SOFT are the internal setting files included in ps2_softemu. They may have codes that don't work on ps2_netemu.
GX are the internal setting files included in ps2_gxemu. They may have codes that don't work on ps2_netemu.