The Emmys have always had a soft spot for nominating programs in their swan-song season, so no one was surprised when “The Sopranos” came up the big winner this year, earning nods for best drama series, best lead actor (James Gandolfini), best lead actress (Edie Falco) and a trio of nominations in the supporting-actor categories (Aida Turturro, Lorraine Bracco and Michael Imperioli). “The Sopranos” also nearly swept the writing category, taking three of the five nominations handed out. Of course, this wasn’t just a nostalgia prize. “The Sopranos” is a history-making television drama.

But the Emmys are a peculiar beast. When a show is nominated for best in its category, it isn’t really the entire show that’s getting nominated—it’s just one episode. There’s way too much television for Emmy nominators to watch everything, so producers submit a single episode of their show, the one they deem representative of the program’s overall quality. Then they cross their fingers and pray they’ve chosen wisely. Sometimes they don’t. Many people in the TV industry believe that this wrinkle in the award process cost “Lost” a best-drama nomination in 2006: its producers submitted a mediocre episode, and the academy turned up its nose.

For the 2007 Emmys, “The Sopranos” submitted its final-season premiere, titled “Soprano Home Movies”—not its controversial finale, “Made in America.” In some ways, it was a safe choice, considering how a certain five seconds at the very end of “Made in America” managed to infuriate half the country. But it was a risk as well: like “Made in America,” “Soprano Home Movies”—in which Tony and Carmela spend a restive weekend at the family lake house with his sister and her husband, Bobby—was not a fan favorite, chiefly because no one important gets whacked. Except for a quick spate of violence at the end of the episode, much of it is quiet and somber. Personally, this was my favorite “Sopranos” episode of the season: set in leafy, natural tranquility, it echoed the beginnings of the show—remember the ducks?—and established a dark foreboding that hung over of the rest of the season like a thundercloud. It was written like a beautiful damning, more of a play than a television episode.

And perhaps more importantly, for Emmy voters, its ending didn’t make viewers think their cable had been disconnected. But even if the show’s producers had chosen to submit the controversial finale, it probably wouldn’t have mattered. There’s no way voters weren’t nominating a TV giant for its final bow. But it’s one thing for “The Sopranos” to get nominated for its final season; it’s quite another for it to win the Emmy for best drama. Even though “Soprano Home Movies” is up for the award, the series’s abrupt ending could leave a bitter taste in voters’ mouths. Especially since all of the other nominees in the category—ABC’s “Grey’s Anatomy” and “Boston Legal,” Fox’s “House” and NBC’s “Heroes”—are popular network dramas, which the Emmys historically tend to favor. Remember, in its six seasons, the mighty “Sopranos” has only won this award once. So don’t rule out an upset.

After winning the best-drama Emmy for its first season in 2005, “Lost” has now been shut out of the category two years in a row. But this time around, “Lost” didn’t lose because its producers submitted the wrong episode. The show’s third season was bumpy to say the least. About halfway through, many fans came close to writing it off entirely. But “Lost” recovered with a thrilling run of episodes at the end of the season, culminating with its instant-classic finale, titled “Through the Looking Glass.” This was the episode that “Lost”’s producers submitted for Emmy consideration.

So what happened? You got me. The Emmys’ odd, single-episode nominating process does put serialized dramas such as “Lost” in a tricky spot. It’s impossible to appreciate an episode like “Through the Looking Glass” if you missed everything that led up to it. That’s why so-called procedurals—programs with self-contained story lines that wrap up in an hour, such as “Law & Order,” “CSI” and, more recently, “House”—have tended to fare well at the Emmys. But the process’s natural bias against serialized shows didn’t hurt “The Sopranos,” or “Grey’s Anatomy.”

And here’s the weird thing about this year’s Emmys: it didn’t exactly hurt “Lost,” either. “Through the Looking Glass” earned well-deserved nominations in both the writing and the directing categories, but the show still failed to earn a nomination for best drama series. In other words, the academy decided that “Lost” was beautifully written and directed, but other than that, they weren’t impressed. “Boston Legal” and “Heroes,” meanwhile, earned only a directing nomination. And “House” was shut out of both writing and directing honors. Yet all three were nominated for best drama.

Of course, the Emmys have always been filled with bizarre quirks and egregious slights. Once again, HBO’s stunning Baltimore crime drama “The Wire”—which so many critics, including this one, have praised so relentlessly that we’re becoming insufferable—failed to earn a single nomination. Zero. Nada. Meanwhile, HBO’s original movie about crimes against Native Americans in the late 1800s, “Bury My Heart at Wounded Knee,” which was so earnest and respectful that it put me to sleep in 20 minutes flat, collected more nominations than any other program on television—animal, mineral or vegetable—with 17 total. The Emmys also have such an endless laundry list of categories that it’s often hard to tell one from the other. Spike Lee’s magisterial, heartbreaking Katrina documentary for HBO, “When the Levees Broke,” was nominated for “Exceptional Merit in Nonfiction Filmmaking,” a new award created in 2005 to honor programs with “profound social impact”—but it was overlooked in the “Outstanding Nonfiction Series” category. Voters evidently preferred “Inside the Actors Studio.”

I’ll spare everyone my grumbling that “Heroes” was nominated for best drama over NBC’s far superior freshman program, “Friday Night Lights,” if only because the presence of “Heroes” in this group shows that Emmy voters are slowly correcting their longstanding bias against newcomers. (Remember when “Frasier” seemed to win best comedy every single year?) Three brand-new shows will compete for the top prizes this year: “Heroes” in the drama category, plus NBC’s “30 Rock” and ABC’s “Ugly Betty” in the comedy category. And voters proved they’re actually paying attention to the ups and downs of old favorites. Last year’s winner in the drama category, “24,” was rightly ignored after a terrible season this time around. We’ll have a new winner when the awards are handed out on Sept. 16, and my prediction is that “The Sopranos” will still get the ending it deserves. But watch out for “House.” In the comedy category, look for “Ugly Betty” to knock off NBC’s defending champ “The Office.” The Emmys haven’t gotten smart, but they are getting hip.