What tools can I find in Ubuntu to flash the firmware of the motherboard or any other hardware from terminal or gui. Specially for those formats that ask for a 3.5 disk (In this time of age??) or other formats made that are troublesome to do.
First, a word of caution, if there is a problem updating your bios or if you make a mistake you might render you computer inoperable / unbootable. I highly advise you start by confirming with your vendor that a bios update is advisable.
Second, some vendors, such as Dell, offer Linux options.
If your vendor only offers a .exe , if at all possible, I would run it from Windows.
There are 3 alternates available to you if you do not run windows:
You will have to download and install biosdisk from here
You then extract the archive and install it
You can then make a .deb with
Flashrom is in the ubuntu repositories and supported hardware is listed here
Make a backup of your current BIOS
Install a new BIOS
Freedos can be installed to a flash drive with unetbootin. You then boot from the flash drive and use the DOS command line to run your bios .exe
The Arch Linux Wiki has a page with additional detail on all these tools.