There have been numerous Biblical references in this series. Below are a few:

OBVIOUS ONES:
1. Eko pretends to be a priest after his brother is murdered trying to help him smuggle heroin. He also carries a stick inscribed with scripture

2. The story of Eko and his brother "echoes" many Bible stories: Jacob and Esau (the birthright), the Prodigal Son
2a. Eko's final face-off with the monster and refusal to be sorry is similar to Cain's reply to God: "Am I my brother's keeper?"

3. One episdoe is entitled "The 23rd Psalm": "The Lord is my shepherd, I shall not want.." which Eko and Charlie recite as the heroin plane burns
3a. Jack's last name is Shepherd; shepherds are referred to as leaders and sources of guidance throughout the Bible
3b. Jack's father's name is Christian Shepherd, perhaps as in "Christian leader or counselor"
3c. Wasn't Abel a shepherd, and also King David (before he was king, or course), and Moses and Amos (one of the prophets) and all those shepherds who heard the angels herald Jesus' birth (although, correcting an earlier contributer's comment, Jesus's stepdad Joseph was a carpenter, not a shepherd).
3d. Jesus refers to himself as 'The Good Shepherd', who gives his life for his sheep.


4. Eko finds part of the orientation reel inside a hallowed-out Bible

5. There is a mysterious Jacob who seems in control. Jacob was husband to Rachel, father of Joseph, and had trouble getting Rachel pregnant
5a. Jacob waited 7 years to marry Rachel because her father wouldn't let him yet (Desmond and Penny?)
5b. Jacob had 4 wives (double-check that). 4 is a number

6. Charlie wanted to be an altar boy, but his brother and herion addiction ruined it
6b. Charlie and Liam also have rocky relationship like Cain and Abel or Jacob and Esau (or almost any pair of Biblical brothers)

7. Claire's baby is named Aaron, like Moses's brother, the more confident, yet quiet, one

8. After murdering Danny and her life was spared, Juliet was "marked". Cain was also marked after he killed Abel.


NOT-SO-OBVIOUS ONES:

1. The hatch mural is reminiscent of the writing on the wall of the king

2. The Island is parallel to the garden of Eden. The two skeletons in the cave during season one (Adam and Eve), the fertility curse (burdened by man after the Fall), mysterious location, pleniful resources ect...

2. The shirt Desmond borrows after the hatch imposion reminds me of Joseph's technicolor dreamcoat :)
2a. Seriously, Desmond has visions of the future not unlike Joseph's visions
2b. Desmond's last name, "Hume", comes from a Latin word for "earth," as in human. The first man, Adam, was made from earth.
2c. Henry Ian Cusick has played Jesus in a movie

3. We have a John and one James (Sawyer's real name is James). Both are names of disciples (and there were two disciples named James).

4. The baby-snatching theme is similar to that of the Egyptians, whose first-born all died when Pharoah was enslaving the Israelites
4a. There was also a mad hunt for Jesus after his birth

5. Season One episode titles include "Numbers" and "Exodus" which are, of course, books of the Bible.