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I want to write a script to enable my program on boot automatically. This can be done using SysV Init, Upstart or systemd. However, I am not able to figure out which init system my Raspbian uses.
Another doubt I have is that, suppose the default init system is upstart, then will a script written and enabled with systemd work? To rephrase, do we need to write init script in the default init system to make it work?
Raspian is basically Debian.
Debian until and including Wheezy/7 used SysV, since Jessie/8 systemd.
Upstart is not relevant anymore, since even RHEL and Ubuntu (the Upstart developers) have moved to systemd.
systemd is very different from sysv. However, there is a compatibility layer in systemd that will transparently create units for properly annotated sysv init scripts on the fly. If you plan to distribute your init script to other raspian users, a well-tested sysv init script will also work in systemd. While systemd is pretty complex, creating services is actually surprisingly simple.
As for the init system on your machine, stat /sbin/init should give you a good indication on Debian. For general initsystem detection, this Unix&Linux question has excellent answers.
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init vs. systemd) can be selected - all my machines (PCs & RPis) use SysV init even though some are using Jessie...! 8-) {For the record do not try to install upstart into an init using Jessie system directly - that breaks very badly... 8-( }