2. Given the early Christian tendency towards asceticism, the wine miracle is an unlikely invention [2:8].
3. Archaeology confirms the proper place of Jacob's Well [4:6].
4. Josephus [Wars of the Jews 2.232] confirms there was significant hostility between Jews and Samaritans during Jesus' time [4:9].
5. "Come down" accurately describes the topography of western Galilee. [There's a significant elevation drop from Cana to Capernaum.] [4:46, 49, 51].
6. "Went up" accurately describes the ascent to Jerusalem [5:1].
7. Archaeology confirms the proper location of Bethesda [5:2]. [Excavations between 1914 and 1938 uncovered that pool and found it to be just as John described it. Since that structure did not exist after the Romans destroyed the city in A.D. 70, it's unlikely any later non-eyewitness could have described it in such vivid detail. Moreover, John says that this structure "is in Jerusalem," implying that he's writing before 70].
8. Jesus' own testimony being invalid without the Father is an unlikely Christian invention [5:31]; a later redactor would be eager to highlight Jesus' divinity and would probably make his witness self-authenticating.
9. The crowds wanting to make Jesus king reflects the well-known nationalist fervor of early first-century Israel [6:15].
10. Sudden and severe squalls are common on the Sea of Galilee [6:18].
11. Christ's command to eat his flesh and drink his blood would not be made up [6:53].
12. The rejection of Jesus by many of his disciples is also an unlikely invention [6:66].
13. The two predominant opinions of Jesus, one that Jesus was a "good man" and the other that he "deceives people," would not be the two choices John would have made up [7:12]; a later Christian writer would have probably inserted the opinion that Jesus was God.
14. The charge of Jesus being demon-possessed is an unlikely invention [7:20].
15. The use of "Samaritan" to slander Jesus befits the hostility between Jews and Samaritans [8:48].
16. Jewish believers wanting to stone Jesus is an unlikely invention [8:31, 59].
17. Archaeology confirms the existence and location of the Pool of Siloam [9:7].
18. Expulsion from the synagogue by the Pharisees was a legitimate fear of the Jews; notice that the healed man professes his faith in Jesus only after he is expelled from the synagogue by the Pharisees [9:13-39], at which point he has nothing to lose. This rings of authenticity.
19. The healed man calling Jesus a "prophet" rather than anything more lofty suggests the incident is unembellished history [9:17].
20. During a winter feast, Jesus walked in Solomon's Colonnade, which was the only side of the temple area shielded from the cold winter east wind [10:22-23]; this area is mentioned several times by Josephus.
21. Fifteen stadia [less than two miles] is precisely the distance from Bethany to Jerusalem [11:18].
22. Given the later animosity between Christians and Jews, the positive depiction of Jews comforting Martha and Mary is an unlikely invention [11:19].
23. The burial wrappings of Lazarus were common for first-century Jewish burials [11:44]; it is unlikely that a fiction writer would have included this theologically irrelevant detail.
24. The precise description of the composition of the Sanhedrin [11:47]: it was composed primarily of chief priests [largely Sadducees] and Pharisees during Jesus' ministry.
25. Caiaphas was indeed the high priest that year [11:49]; we learn from Josephus that Caiaphas held the office from A.D. 18-37.
26. The obscure and tiny village of Ephraim [11:54] near Jerusalem is mentioned by Josephus.
27. Ceremonial cleansing was common in preparation for the Passover [11:55].
28. Anointing of a guest's feet with perfume or oil was sometimes performed fro special guests in the Jewish culture (12:3); Mary's wiping of Jesus' feet with her hair is an unlikely invention [in easily could have been perceived as a sexual advance].
29. Waving of palm branches was a common Jewish practice for celebrating military victories and welcoming national rulers [12:13].
30. Foot washing is first-century Palestine was necessary because of dust and open footwear; Jesus performing this menial task is an unlikely invention [it was a task not even Jewish slaves were required to do] [13:4]; Peter's insistence that he get a complete bath also fits with his impulsive personality [there's certainly no purpose for inventing this request].
31. Peter asks John to ask Jesus a question [13:24]; there's no reason to insert this detail if this is fiction; Peter could have asked Jesus himself.
32. "The Father is greater than I" is an unlikely invention [14:28], especially if John wanted to make up the deity of Christ [as the critics claim he did].
33. Use of the vine as a metaphor makes good sense in Jerusalem [15:1]; vineyards were in the vicinity of the temple, and, according to Josephus, the temple gates had a golden vine carved on them.
34. Use of the childbirth metaphor [16:21] is thoroughly Jewish; is has been found in the Dead Sea Scrolls [1QH 11:9-10].
35. The standard Jewish posture for prayers was looking "toward heaven" [17:1].
36. Jesus' admission that he has gotten his words from the Father [17:7-8] would not be included if John were inventing the idea that Christ was God.
37. No specific reference to fulfilled Scripture is given regarding the predicted betrayal by Judas; a fiction writer or later Christian redactor probably would have identified the Old Testament Scripture to which Jesus was referring [17:12].
38. The name of the high priest's servant [Malachus], who had his ear cut off, is an unlikely invention [18:10].
39. Proper identification of Caiaphas's father-in-law, Annas, who was the high priest from A.D. 6-15 [18:13]-the appearance before Annas is believable because of the family connection and the fact the former high priests maintained great influence.
40. John's claim that the high priest knew him [18:15] seems historical; invention of this claim serves no purpose and would expose John to being discredited by the Jewish authorities.
41. Anna's questions regarding Jesus' teachings and disciples make good historical sense; Annas would be concerned about potential civil unrest and the undermining of Jewish religious authority [18:19].
42. Identification of a relative of Malchus [the high priest's servant who had his ear cut off] is a detail that John would not have made up [18:26]; it has no theological significance and could only hurt John's credibility if he were trying to pass off fiction as the truth.
43. There are good historical reasons to believe Pilate's reluctance to deal with Jesus [18:28ff.]: Pilate had to walk a fine line between keeping the Jews happy and keeping Rome happy; any civil unrest could mean his job [the Jews knew of his competing concerns when they taunted him, "If you let this man go, you are no friend of Caesar. Anyone who claims to be a king opposes Caesar," 19:12]; the Jewish philosopher Philo records the Jews successfully pressuring Pilate in a similar way to get their demands met [To Gaius 38.301-302].
44. A surface similar to the Stone Pavement has been identified near the Antonia Fortress [19:13] with markings that may indicate soldiers played games there [as in the gambling for his clothes in 19:24].
45. The Jews exclaiming, "We have no king but Caesar!" [19:15] would not be invented given the Jewish hatred for the Romans, especially if John had been written after A.D. 70. [This would be like New Yorkers today proclaiming "We have not king but Osama Bin Laden!"]
46. The crucifixion of Jesus [19:17-30] is attested to by non-Christian sources such as Josephus, Tacitus, Lucian, and the Jewish Talmud.
47. Crucifixion victims normally carried their own crossbeams [19:17].
48. Josephus confirms that crucifixion was an execution technique employed by the Romans [Wars of the Jews 1.97; 2.305; 7.203]; moreover, a nail-spiked anklebone of a crucified man was found in Jerusalem in 1968.
49. The execution site was likely outside ancient Jerusalem, as John says [19:17]; this would ensure that the sacred Jewish city would not be profaned by the presence of a dead body [Deut. 21:23].
50. After the spear was thrust into Jesus' side, out came what appeared to be blood and water [19:34]. Today we know that a crucified person might have a watery fluid father in the sac around the heart called the pericardium. John would not have known of this medical condition, and could not have recorded this phenomenon unless he was an eyewitness or had access to eyewitness testimony.
51. Joseph of Arimathea [19:38], a member of the Sanhedrin who buries Jesus, is an unlikely invention.
52. Josephus [Antiquities 17.199] confirms that spices [19:39] were used for royal burials; this detail shows that Nicodemus was not expecting Jesus to rise from the dead, and it also demonstrates that John was not inserting later Christian faith into the text.
53. Mary Magdalene [20:1], a formerly demon-possessed woman [Luke 8:2], would not be invented as the empty tomb's first witness; in fact, women in general would not be presented as witnesses in a made-up story.
54. Mary mistaking Jesus for the gardener [20:15] is not a detail that a later writer would have made up [especially a writer seeking to exalt Jesus].
55. "Rabboni" [20:16], the Aramaic for "teacher," seems an authentic detail because it's another unlikely invention for a writer trying to exalt the risen Jesus.
56. Jesus stating that he is returning to "my God and your God" [20:17] does not fit with a later writer bent on creating the idea that Jesus was God.
57. One hundred fifty-three fish [21:11] is a theologically irrelevant detail, but perfectly consistent with the tendency of fisherman to want to record and then brag about large catches.
58. The fear of the disciples to ask Jesus who he was [21:12] is an unlikely concoction; it demonstrates natural human amazement at the risen Jesus and perhaps the fact that there was something different about the resurrection body.
59. The cryptic statement from Jesus about the fate of Peter is not clear enough to draw certain theological conclusions [21:18]; so why would John make it up? It's another unlikely invention. 
Frank Turek and Norman Geisler, I Don't Have Enough Faith to be an Atheist, p. 263-268