Most of the characters in Star Trek are atheist. The Klingons are like Sikhs living by guidelines of a the first Klingon rather than their gods. Romulans and Vulcans are atheist. Humans are atheist as are the Dominon and Cardassia. Infact the Bajorans are regarded as "really backwards religious extremists" for their belief. The borg can be argued as believers in spinoza's god (order and mechanism) rather than outright atheists.
Religion isn't even mentioned bar the bajorans (however this is a universe where a lot of woo exists either as a function of technology or novel physiology) and any spirituality is done solely for cultural reasons. Chakotay does not count since by the equivalent of the universe the man is a raging religious lunatic.
Star Trek is incredibly atheist including the very first episode of TNG where Picard meets an actual "God" and regards him as another alien species rather than as a deity to be worshipped actively defending actions rather than kowtowing to him. (It's a very enlightened show. We look at the original series and Uhura is technically one of the earliest instances of a black person on a show in any job of power. She is the third highest ranked person on the ship. Also one of the first interracial romances were shown as completely natural.)
The Characters in MASH were highly irreligious and probably lapsed christian. Infact I regard MASH as one of the best medical shows out there.
As "atheist" movie characters are meant to go John Constantine is supposed to be one but sadly the movie forgot completely.
Gregory House is an atheist (as is Hugh Laurie himself)
Colossus is an atheist (X-Men)
So plenty exist. We aren't that common IRL ourselves so it's a pretty decent selection.
How could I forget about that show?! I love it!
I don't recall any specific comments they have made about being atheists.
I know that Howard (or at least his mother) is Jewish. Sheldon's mom is a Texas bible-thumper. Raj is a Hindu. Don't know about Leonard.