The $45 million libel trial of Moral Majority leader Jerry Falwell versus sex magazine publisher Larry Flynt under way in federal court here this week has it all: suspense, comedy, pathos, videotapes and dramatic speeches from a theatrical New York lawyer.

Today, day three, it also included a last-minute, behind-the-scenes appearance from Flynt, the self-described "Duke of Raunch," who arrived in town yesterday but stayed away from court. Flynt told reporters after adjournment that he has no illusions about winning the case in conservative Southwest Virginia and that he has no apologies.

"The ad was a parody," he said. "We said it was a parody and not to be taken seriously." Flynt said that jurors should remember the issue is libel and not the tenor of his magazine. "This is a libel case, not an obscenity case. I know I'm in the minority. I know I'm not everybody's cup of tea. But, I have a significant readership . . . . "

Of his possible appearance on the stand Thursday, he said, "I'm going to be myself. That's one thing people can say about me that they can't say about Jerry Falwell. I'm me, and he should admit that he's a politician and not a preacher."

The final witnesses for Falwell were called today and Flynt's attorneys made their opening statements.

The trial has been described by Falwell as a confrontation between good and evil. It also happens to be the best show in town this week and has played to a packed courtroom every day.

Falwell, the charismatic leader of the conservative Moral Majority and star of a multimillion-dollar radio and television ministry, is suing Flynt, his sex magazine, Hustler, and his publishing company over a liquor advertisement parody that purported to quote Falwell saying that he often gets "sloshed" before preaching and that his first sexual experience was with his mother. The ad appeared in two issues of Hustler and prompted Falwell to sue for libel, invasion of privacy and intentional infliction of mental distress.

Flynt's attorneys have contended that the appearance of a small-type disclaimer that ran at the bottom of the page, advising readers that it was a parody and not to be taken seriously, absolves Flynt and the magazine of any libelous intent. Falwell's attorneys have spent the last three days presenting evidence that attempts to show a pattern of malice against their client.

While Falwell, 50, has been giving interviews all week, Flynt, 42, has kept curious onlookers in suspense. Would he appear or wouldn't he? At times, even U.S. District Judge James C. Turk didn't appear to know.

The eight-woman, four-man jury has had to content itself with two showings from a three-hour videotaped deposition taken last summer, during which Flynt held forth from a prison hospital gurney. The Kentucky-born Flynt has been paralyzed from the waist down since 1978, when he was shot three times while attending a trial on obscenity charges in Lawrenceville, Ga.

In that videotape, Flynt stated repeatedly that the ad parody was intended to be taken as truth, and that he had photographic evidence that the descriptions of incest were fact.

Today, Flynt's lawyers told the jurors that their client's claims should be disregarded and that the deposition should be regarded as evidence of Flynt's mental illness. They said he is under treatment for chronic mania and that he has undergone electric shock therapy treatment.

Flynt appeared calm and lucid during a late afternoon interview with reporters. His appearance in a brown pullover, brown pants, high-topped sneakers and sitting in a wheelchair in his suite at the Marriott Hotel was a pronounced contrast with the bearded, profane man who appeared in the videotape.

Flynt explained that the deposition had been taken at a time when he was physically uncomfortable and angry at what he described as mistreatment from prison authorities and lawyers.

Falwell has said repeatedly that he believes Flynt is sane and clearly meant him harm.

Falwell is seeking punitive and compensatory damages, arguing that the ad damaged his reputation. Flynt's lawyers have countered that Falwell used a censored version of the parody in a mail solicitation that raised $800,000 last year. "Why, if I damaged his reputation so bad, why did Ronald Reagan ask him to deliver the benediction at the Republican National Convention?" Flynt asked. "How can he sit there with a straight face and say I damaged him?"

Flynt told reporters he is not expecting to win this round. "I hope I'm wrong, but I'm a realist. I could sit here and give you some phony kind of testimony about how I'm optimistic, but I'm not."