If you want to start daemons or programs to start in the background, check /etc/init.d directory and /etc/rcX.d folders (and run the runlevel program to check your current runlevel). And also check /etc/inittab as init is controlling everything in boot time...
by the way, run and runonce has nothing to do with the Windows kernel.
There are startup-time programs, check them in the mentioned /etc/rcX.d dirs. (They are runlevel based init and stop commands, linked to the scripts residing in /etc/init.d).
There are login-time programs, their control is determined by your shell, e.g. if you are using bash then check .bash_profile (for login shell) and .bashrc (for interactive shell).
So, autoexec.bat can be integrated as the part of the shell scripts mentioned above...
to begin get started with some reading:
Linux/Unix shouldn't be handled as a click-and-play OS, there are endless possibilities just take a very little time to __understand__ it in the basic, console level.
Hope I could help.