IAST is the most frequently used standard for transliterating Sanskrit and the one generally taught in textbooks. Individual authors may adopt there own ad hoc variants, such as using ṁ instead of ṃ for the anusvāra, or using r̥ instead of ṛ for ऋ. Indeed, some authors may prefer to use full ISO-15919 (which is really overkill for Sanskrit, because it allows representation of characters simply not found in Sanskrit). But these minor differences can easily be accommodated for.
This is the preferred professional standard. It is true that in older books or online, where such characters are more difficult to produce, ASCII-only systems like Harvard-Kyoto may still be employed. But if you're wondering which to learn, or which to use, I suggest IAST.
Also, technically, Hunterian is the standard officially used by the Indian government, but - again - this is not widely adopted for Sanskrit, especially outside of India and the system does not distinguish many characters.