Since the you are talking about rating, not price, that is what I'm going to go with. I'll start out by saying that I disagree with almost every one of your examples, especially with Total Nuclear Annihilation. I have no idea how that game put you to sleep. I would agree that World Cup Soccer is underrated.

I'm just going to go down list and comment on what I rate quite a bit differently then the consensus.

##Overrated##
Pirates of the Caribbean - I find this game to be overrated. It's a good game, but it's well outside of my personal top-10.
Batman (The Dark Knight) - It's outside of the top-100, but I'd put it even lower.
F-14 Tomcat - You could argue that all System 11 games are underrated. I'm okay moving them all up, but F-14 would be near the bottom of that list for me.
The Pinball Circus - I'm going to play it at the Pinball Hall of Fame because it's different. It's different, but not that good.
South Park - It's dropped a lot on the list, but it's still overrated. Beyond the theme, it's not a fun game to shoot.

##Underrated##
The Shadow - Should be one of the top-tier games IMHO.
Fish Tale - I call it my guilty pleasure game. I currently have it rated as my second favorite game of all time.
Congo - Add this one to the list of games I regret selling.
Indianapolis 500 - I enjoy the three games listed above more, but Indy 500 is underrated too.
Stars (Stern) - I could probably fill an underrated list with pre-90s games, but Stars just happens to be one of the best from that long list.
World Poker Tour - I solid game. Should easily be in the top 200.
Lethal Weapon 3 - Again, I'm shocked it outside of the top 200.
Godzilla - Ditto
Monopoly - Ditto
Wheel of Fortune - Ditto
WWE Wrestlemania - I'm not sure why I like this game, but I really do have fun playing it.
Hardbody - I assume it has to be the theme. The game shoots pretty good.

##Just Comments##
Batman 66 - The game has grown on me the more I play it. I originally had it much lower, but I'm okay where it's listed at this point.
Rick and Morty - I'm fine with it's overall rating, but it's my third favorite Spooky title. I guess that means TNA and ACNC are underrated.

I think what it comes down to is that I really just like pinball. If I just used the basic Pinside ratings of Excellent, Good, Decent, Not So Good, Poor, Terrible most games would be "Good" or better. Sure I could argue this games better then that game, but you're nitpicking at that point when in reality there are just a lot of great games.

So for a bit of fun, I compared my rankings with those on Pinside. I tried to only include games I know really well. Some confirmed how I felt about the game, but there are quite a few examples where games I really love are considered "overrated". I guess others love them more then me. I think what it could be is there is some element of the game such as art, theme, or toys that I rated a bit lower. If I could completely customize my own rankings "fun" would be worth 75% of my total score. That's where games a game like Deadpool really shines. I don't love the layout, but it's fun to shoot.

##Overrated##
Pinball Circus (7.3 / 5.3) - No surprise. I feel like it's hyped because it's rare and different.
South Park (7.1 / 5.5) - Yeah, I can walk away mid-ball.
F-14 Tomcat (7.5 / 6.0) - System 11s are mostly underrated. F-14 is the exception. I have on need to own another.
Batman: The Dark Knight (7.7 / 6.3) - One of the worst Stern titles of all time.
Pirates of the Caribbean (8.8 / 7.8) - I really do like this game. I just don't seem to love it as much as everyone else.
Pinbot (7.8 / 7.0) - Now we have some that I was shocked were on the list. Pinbot is a solid game. A good bang for your buck.
Alice Cooper's Nightmare Castle (8.3 / 7.5) - Man, this one hurts. I really like the game.
AC/DC (8.5 / 7.8) - I'm fine with this one on the list. It's solid, but not that great.
Batman 66 (8.4 / 7.7) - This game has grown on me quite a lot. I still am not a huge fan of the layout, but the rules are great.
Ghostbusters (8.4 / 7.7) - Yeah, this makes sense. The geometry is off just enough to be annoying.
Judge Dredd (8.0 / 7.4) - Another game I like, but there are much better 90s games that are rated lower. Still a good value.
Star Trek: The Next Generation (8.5 / 7.9) - Surprised this made the list. I'd own one again. I enjoy playing it.
Rick & Morty (8.4 / 7.6) - I'm a lot more upset that Alice Cooper made the list. It's a tad overrated. Great theme integration.
Rob Zombie's Spookshow International (7.5 / 7.0) - It's a bit rough for me. I do really like Spooky games, I promise.
Deadpool (8.7 / 8.2) - From her on down my statistical attempt at this feels like complete BS. I love all these games.
Bram Stoker's Dracula (8.2 / 7.7) - Great game. Owned in the past and would own again.
Jurassic Park (8.5 / 8.1) - Great game. I have one on order.
Iron Maiden (8.6 / 8.1) - Great game. It's on my wanted list.

##Underrated##
Hardbody 5.7 / 7.4) - I stand by this. If I had more room I'd own more late 80s games.
Fish Tales (8.0 / 9.0) - Yep, it's one of the best games of all time.
Attack from Mars: CE (8.5 / 8.8) - Specifically the CE is underrated. I have it rated the same as the original.
Twilight Zone: (8.7 / 9.0) - Hardly worth mentioning, but all my rankings seems lower then averages.
Metallica (8.7 / 9.0) - One of my favorites.
WWE Wrestlemania (7.2 / 7.5) - This is one where it's underrated for gameplay, but perhaps still overvalued.
Stars (7.5 / 7.7) - I wish this was higher. Stars is great.
Congo (8.0 / 8.2) - Another game I would love to own again. I really like the diamond collection rules.