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1.
This is based on the Biblical New Testament story where Thomas, one of the apostles of Christ, refused to believe that Jesus had risen from the grave without seeing evidence. On seeing this evidence, he praised those who believed without proof.

Typically this phrase is used in a midly derogatory. It describes someone who refuse to simply believe in something out of pure faith without asking for evidence. A devout Christian might consider me to be a doubting thomas because I don't believe there is a God since there's no evidence. The Christian considers it a bad thing that I'm not simply willing to have some faith.
Fanatic: How can you not believe in God? You don't want to be a doubting thomas?
Athiest: Normal people don't consider it a bad thing when others ask for proof when they make extraordinary claims. If I said that I am Zrlak, King of Mars, I would have little respect for you if you believed me without asking for evidence yet you expect me to just believe your equally ridiculous claims?
by thepreacher November 18, 2005
 
2.
A person who does not trust his/her best friend, even though the best friend has proven them self to be virtuous.
"My best friend won't trust me with his sister"

"Dude, He is such a Doubting Thomas"

"Yeah, I feel kinda Judased
by Foster John February 20, 2010
 
3.
a raw band with kenzies brother in hes a nex man called rory!
man im goin to see a rad doubtin thomas gig in esquires!
by MC givern March 08, 2005