There really is no right or wrong here. It's all about what sound you're after and what chord comes next.

If you switch between a standard C chord and G, #3 will make the transition smoother.

#2 is great for electric guitar if you also fret the 3rd fret of the B string. When you have a bit of crunch/gain on this sounds less muddy since we omit all thirds. It essentially becomes a G power chord.

I personally never use #1. I always add the 3rd fret of the B string.

I sometimes play the 3rd fret on the low E string with my thumb, muting the A string, and I fret the 3rd fret of the B string with my ring finger, and the 3rd fret of the high E string with my pinky.

Practice all of them :D