What religious references did Thomas Jefferson put in the Declaration of Independence.?

Answer 1

I note that you asked what references JEFFERSON made. This is not the same thing as "what religious references are IN the Declaration", since the Declaration Committee Jefferson chaired, and then the whole Congress, did make some changes.

So I'll list ALL the religious references found at various stages, as well as their source (known or surmised):

1.) (Opening paragraph) ". . . the equal and independent station to which the laws of nature and of NATURE'S GOD entitle them" = Jefferson (original draft)

2.) (Second paragraph) Original reads: "We hold these truths to be [sacred and undeniable] selfevident, that all men are created equal and independent; that from that equal creation they derive in rights inherent and inalienable"

CONGRESS added "endowed by their CREATOR" - so strengthening the RELIGIOUS reference

3.) (Toward the end of the list of 'charges' against the King) -- Jefferson originally wrote a strong charge blaming the King for the slave trade, including the following:
"he has waged cruel war against human nature itself. . . this piratical warfare, the opprobium of INFIDEL powers, is the warfare of the CHRISTIAN king of Great Britain."

Jefferson's use of "Christian" here (along with "infidel") is ironic -- mocking the King as not behaving Christian-ly

But this whole section was deleted from the final version, due to the objection of the Southern colonies

4) (Conclusion)
Original - "We, therefore, the representatives of the United States of America, in General Congress, assembled . . . And for the support of this declaration we mutually pledge to each other our lives, our fortunes and our sacred honor."

Congress here added explicit religious references as the beginning and end:
"We, therefore, the Representatives of the United States of America, in General Congress, Assembled, APPEALING TO THE SUPREME JUDGE OF THE WORLD for the rectitude of our intentions. . . And for the support of this Declaration, with a firm reliance on the PROTECTION OF DIVINE PROVIDENCE, we mutually pledge to each other our Lives, our Fortunes and our sacred Honor.

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Here seems to be the closest we can get to Jefferson's ORIGINAL text --
http://odur.let.rug.nl/~usa/D/1776-1800/independence/doitj.htm

Compare these with images of the manuscript as it seems to have come from the Committee, with some changes. Many of these are in Jefferson's hand, some look like they might be written in my John Adams -- though even for the changes Jefferson himself wrote it is unclear whether they were his own idea, of the suggestion of another (likely Franklin or Adams).
http://www.loc.gov/exhibits/treasures/trt001.html

Here is a copy of the text, showing Congressional changes from the Committee version.
http://www.ushistory.org/declaration/document/congress.htm

And finally, the official version of the Declaration as passed by Congress:
http://www.ushistory.org/Declaration/document/

Answer 2

At least 3 times. Pretty good for an Atheist, or was he a Deist, or did he believe in God?

the separate and equal station to which the Laws of "Nature and of Nature's God" entitle them, a decent respect to the opinions of mankind requires that they should declare the causes which impel them to the separation.
This philosophy of natural law was that God created man, god gave man inalienable rights, and man created government. Interesting that now rights come from God, government tells man what to do and man and government are trying to throw God off.

We hold these truths to be "self-evident", that all men are "created" equal, that they are endowed by their "Creator" with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness. --That to secure these rights, Governments are instituted among Men, deriving their just powers from the consent of the governed,
Again rights granted from God to man to government.

with a firm reliance on the protection of divine "Providence", we mutually pledge to each other our Lives, our Fortunes and our sacred Honor.
How could he be a deist (who believe God created man then just sits back and doesn't get involved) if he asks for protection from God in their endeavor of freedom?

Answer 3

Natures God
all men are created equal and endowed by their creator
appeal to the supreme Judge of the World