WebbotLib Studio supports the following software boot loaders:-
FBoot Version 1.2
This boot loader can be problematical if you try to use it while you still have an ISP hardware programmer plugged into the board at the same time. This arises because the ISP (notably the AVRISP MkII) resets the chip about a second after power up and this possibly interrupts the programming process causing it to fail. Similar issues can happen if your power supply is turned on via a switch with a lot of contact bounce.
This is my own boot loader which is loosely based on FBoot and was principally written to overcome the FBoot issue mentioned above.