I play acoustic mostly 3 ways, with a flat pick, with the back of my nails or with the pads of my fingers. All three give you distinctly different sounds. The back of the nails tends to have a mellower tone that a flat pick does and on some songs, it just sounds better to me. When I play with the pads of my fingers, sometimes I like to pull just slightly from underneath the string and give it a little snap, which adds to the tone.
When I use picks, I am very deliberate about the choice of pick, because they also produce different tones. I use a real soft nylon thinner pick for light strumming. I use a thicker harder pick when I want a palm muted rock tone. I use thicker picks for single note soloing. This is all for recording purposes of course, to get specific tones. Live, I just use my favorite pick for everything.
On electric guitar, its picks and pads of fingers. On bass, it can be fingers, thumb, or pick. In all circumstances, the tone that fits the song is what I am after.