I have seen most of the circuit using 12V supply, is there any reason behind this?
Is there any reason to choose 12V in all systems like battery-powered devices?
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I don't find this statement to be true at all: most cell phones have a 3.2V, 3.6V, or 3.7V battery, a lot of small electronics use 1, 2, or 4 AA/AAA batteries (1.5V, 3V, 6V or associated 1.2V multiples with NiMH), quite a few laptops I've used have had ~10.5V battery packs, and I've seen a plethera of 9V batteries used for small electronics as well. I've also used 7.2V NiCd packs for RC applications. About the only thing I commonly use which uses 12V is automotive stuff.
These voltages are dictated by a combination of system component requirements and fundamental physics of the battery cells. For example, Li-Ion cell chemistries give ~3.6-3.7V, and have pretty good energy densities, making them good choices for devices which don't draw a lot of power, but should last for a long time like cell phones.
In the "old days" before lithium, Nicad, nickel-metal hydride and so on the dominant battery technology was lead-(sulphuric) acid. A lead acid cell creates a potential of 2.1 volts. Also, electronics of the time tended to need higher operating voltages. 12 V turned out to be the most useful and the convention has stuck.