There are obviously various definitions for the thickness of a planet's atmosphere. Atmospheric pressure and density drop roughly exponentially with height, $\rho = \rho 0.exp(-h/H)$. One can quote the characteristic scale height, $H$, over which this occurs. This is the height that the atmosphere would abruptly end if the density at the surface, $\rho 0$, were maintained all the way up.
For Earth, $H$ is about 8500 meters. Mount Everest is 8850 meters high, so by that definition it does poke out of the atmosphere, but barely.
For Mars, $H$ is about 11100 meters. Olympus Mons is about 21000 meters high, so by that definition it sticks out about twice the height of the atmosphere
For Venus, $H$ is about 15900 meters. Maxwell Montes is about 11000 meters high, so it sits well inside Venus' atmosphere
For Titan, $H$ is about 21000 meters. Mithrim Montes is only 3337 meters high so it stays right at the bottom of Titan's atmosphere.
Scale height is given approximately by $H = kT/mg$, where $k$ is Boltzmann's constant, $T$ is temperature, $g$ is local surface gravity, and $m$ is the mean mass of a molecule of the atmosphere.
The height of mountains is much more tricky. The work required to create a mountain will be proportional to $g$, so large planets with high surface gravity will tend to have smaller mountains. But the dynamic processes that create mountains will vary very much with the nature of the planet. Olympus Mons on Mars is a very large shield volcano that appears to have been active within the last few million years. The thin atmosphere probably results in little erosion and the relatively thick rigid crust and light gravity will likely mean relatively little hydrostatic subsidence over many eons.