I am setting aside all the confusing Prem/LE ect. considerations. Certainly open to debate because people just list their favorite games and most people's experience with a game is confined to their pinball circle, myself included.
1st
Metallica just never gets old. I am confident that Metallica is Sterns best design up to this point in the company's history but that could always change. I have around 2500 plays on that game.
2nd
As an overall whole, I would say that LOTR was certainly Sterns best game UP TO THAT POINT in the company's history. The company was on the edge of bankruptcy back then and they really pulled out a gem. After playing it hundreds of times, it begins to become a grind where your hands and arms get tired. Once you can get up to 200 mil on that game, for me it loses it's excitement factor. But, it's still #2, even if you can't stand it.
Reasoning for other games that are not 1 and 2:
I know a lot of other great games have come out in between those two and I have owned and played the hell out of a lot of them, but you really have to wait about 4 years on a title to see if it shakes out as "the best". If you are asking about why, just say to yourself, "I should wait until there are no more major code updates, then wait a couple years for everyone to re-asses, then make an informed decision about "the best". So, roughly speaking ~ 4 years from release date.
GOT: Needs some more time but I'd say it's further up the chart on depth than most people even realize. It's just not an adventure style depth, it's more of a points vs. rule exploitation and recognition depth. In some ways, it reminds me of a choose your own adventure video game where you don't mind playing through it again and again because you can approach it a million different ways.
Tron was great but it's really difficult for a new person in pinball to step up to and experience more than a couple minutes of play. And the depth in that game is just not there and was not meant to be there. It's designed for short ball times and that is just never going to appeal to everyone. Iron man, same things.
Star Trek: Certainly some unique things but it's a very safe inside the box design and the callouts are bad, especially if you are not a fan of the newer movies. It think you have to play this one a lot and once you get close to the billion point range, and you've played through all the modes three times, the game certainly does begin to tire. I personally like this game more than GOT, Tron, and LOTR for different reasons but set those opinions aside when contemplating "the best".
AC/DC: The sound is probably the best done in the history of pinball. However, the risk reward is there but there are other design issues that force great players to only follow a couple different paths in the game. Under utilized lower PF on the Prem and over emphasis on VIPs and other things hold it back.
-Spiderman is great and has not been mentioned. I think it's a great game but suffers from some of the same monotony of LOTR after hundreds of plays.
Regarding TSPP, I have played it 1,000s of times. Thousands, not a typo. It's a good game but after you play it for years, you begin to see it's flaws and that it is an early Stern that has some issues regarding design, overall flow, risk/reward and callouts missing from the female characters in the show.
-WPT is great but certainly has some issues that really only bothered me after playing A LOT of games on it - artwork aside...
If you go strictly by Stern sales #'s I am fairly certain it goes something like:
1. ACDC Prem
2. TSPP
3. POTC
So there is CERTAINLY one person who thinks those are the best Stern machines... his name is Gary Stern. 
Cherry Hills Village, CO
