Documentation

Using the GoTek Batch Management Tool
Using the GoTek Batch Management Tool (video)
New Floppy Emulator Does Not Seem To Work

Software

Batch Management Tool (ipcas Floppy Emulator_1.31T)
Batch Management Tool (ipcas Floppy Emulator_1.40i)

FlashFloppy

For using floppy images on a Fat32 formatted USB-stick.
FlashFloppy Wiki
Howto: flash a Gotek with no programmer

FlashFloppy on the Amiga

All needed info is on the FlashFloppy site, but here is the short version just getting started:
Put the jumper on the S0 block, put the spare on J5-JA or just on a single pin (all other positions should be empty): image
From the FlashFloppy archive, copy HxC_Compat_Mode/Amiga/AUTOBOOT.HFE and HxC_Compat_Mode/HXCSDFE.CFG to the root of the USB-stick.
Put floppy images in whatever order you like. You can use sub folders to better organize the images.
To select which image corresponds to which display (001-999) position, you boot on the selector image (000).
Cortex / HxC selector (video)
FlashFloppy selector (video) PC to Amiga with Gotek / Flash Floppy & Amiga Explorer

FlashFloppy on the Atari

As for the Amiga, but copy the Atari HxC_Compat_Mode file instead.

FlashFloppy on the PC (without FF.CFG)

All needed info is on the FlashFloppy site, but here is the short version for just getting started:
Put one jumper on the S1 block and another on on JC (all other positions should be empty): image
Without any further configuration, you can put the disk images on the USB-stick's root to get these automatically recognized. These images are ordered alphabetically, so if you have "Disk1.img", "Disk2.img", "Disk3.img" on the USB, and then add "Another.img", "Another.img" will be the new first one (000).

ADFView

ADFView - For // viewing contents of / copying files from and to / creating new // .adf (Amiga disk dump) images from windows

Other resources

http://tech.webit.nu/amiga-floppy/
http://tech.webit.nu/amiga-hardware/
http://tech.webit.nu/amiga-emulation/