Johnny probably gets about as much respect as he deserves, because he's permanently stuck in "immature teenager" characterization mode.

Ben's unique in that he's one of the strongest characters in the Marvel Universe, but a lot of fans and many of the writers don't understand how smart and experienced he is. he entered the series as a war veteran, he's got a degree from the same college that Reed and Doom attended, and he was a professional test pilot with some boxing and wrestling experience. Ben's got a pretty decent power set, but what sets him apart is his willpower, fighting prowess, and applied intelligence. the basic test for what separates a great FF writer from a decent to mediocre one is whether or not they realize that Ben is the smart one on the team.

for my money, the Waid & Weiringo run on the book is one of the best:
https://www.amazon.com/Fantastic-Four-Wieringo-Ultimate-Collection/dp/0785156550

Fantastic Four

• Fantastic Four | #60-70, 500-524 | 2002-2005 | Waid
  
• Fantastic Four, FF | #570-588, 600-611, 1-23 | 2009-2012 | Hickman | Reading Order
  
  

  Spider-Man
  

  
        Ultimate Spider-Man | #1-160 | 2000-2008 | Bendis
  
  

• Self-contained Ultimate universe where new readers can start with the very first issue and not miss anything. Hits on all major teenage Spider-Man story beats, friends, and villains. Considered one of the best modern Spider-Man runs of all time.
  
        Spider-Man: Blue | #1-6 | 2002 | Loeb
  
  
• Short, beautiful, touching, heart-warming story about a young Peter Parker torn between two romantic interests and maturing emotionally. Only 6 issues = a low-commitment peek at the character for new readers.
  
        Amazing Spider-Man | #30-57, 500-545 | 2001-2007 | Straczynski
  
  
• JMS' Spidey run is well-regarded for understanding the character being an average guy trying to figure stuff out and make things work. It's dark, funny, dramatic, well-paced, and introduces some new status quo/mythos, even some supernatural elements.
  
        Amazing Spider-Man (Brand New Day) | #546-647 | 2008-2010 | Slott, et al.
  
  
• A fresh start for Peter Parker after Civil War. His memory has been reset and everything is new/different. He's back to his roots: struggling to pay rent, learning how the world works, and fighting his rogue gallery. Closest thing to a "reboot" Amazing Spider-Man has ever had = new reader friendly.
  
        Amazing Spider-Man (Big Time) | #648-700.5 | 2010-2013 | Slott, et al.
  
  
• Peter Parker is back in his groove, he's leading the Avengers, has a new girlfriend, and landed a major career opportunity. This eventually sets up one of the coolest modern Spidey stories in Superior Spider-Man below.
  
        Superior Spider-Man | #1-33 | 2013-2014 | Slott, et al.
  
  
• An impostor takes over for Spider-Man. Very different from the usual Spider-Man characterization = refreshing.

This would be a great place to start. Very recent, great retelling of the origin.

I'll just list the first volume of each series, as they're similarly titled and easy to find on Amazon/wherever if you're looking. (Except Hickman...)

Stan Lee / Jack Kirby: Started it all, still the best. There's the Masterworks paperbacks (about 10 issues a trade) and the omnibus.

• Marvel Masterworks: Fantastic Four, Vol. 1 (Lee / Kirby)
  
• Fantastic Four by Lee & Kirby Omnibus, Vol. 1
  
  John Byrne: The next great run. Again, there're the Visionaries trades and the omnibus.
  
  
• Fantastic Four Visionaries: John Byrne, Vol. 1
  
• Fantastic Four by John Byrne Omnibus, Vol. 1
  
  Walt Simonson: Just trades, as far as I can tell. They also seem to be out of print. (Not a particularly high-priority run, though, so don't worry about it.)
  
  
• Fantastic Four Visionaries: Walt Simonson, Vol. 1
  
  Mark Waid / Mike Wieringo: One of the top runs, easily. Right up there with Lee/Kirby and Hickman.
  
  
• Fantastic Four by Waid & Wieringo Ultimate Collection, Vol. 1
  
  Jonathan Hickman: Recently ended, but already hailed as a landmark. The reading order is a little convoluted because there were two titles at one point. I'll list everything here. (Note: It's all been neatly ordered for the omnibus, so that's the easiest.) Hickman's run starts with a mini-series that tied into the ongoing Marvel status quo at the time, Dark Reign. Norman Osborn, formerly Spider-Man's nemesis the Green Goblin, is given control of the nation's security, starting a SHIELD replacement called HAMMER. While a tie-in, it does set up a major conceit of Hickman's run and I'd recommend reading it. Hickman starts on the book proper with #570 and continues until its cancellation at #588. The book is restarted as FF with a new #1. After #11 of that series, Fantastic Four is brought back with #600, while FF continues its own numbering. This is where things get tricky. Now that there are two titles written by the same guy about mostly the same characters, the reading order is a little wonky. The trades don't even attempt to address this, but I've provided Hickman's recommended order (which was used for the omnibus.)
  
  
• Fantastic Four by Jonathan Hickman Omnibus, Vol. 1
  
• Dark Reign: Fantastic Four (DR:FF #1-5)
  
• Fantastic Four by Jonathan Hickman, Vol. 1 (F4 #570-574)
  
• Fantastic Four by Jonathan Hickman, Vol. 2 (F4 #575-578)
  
• Fantastic Four by Jonathan Hickman, Vol. 3 (F4 #579-582)
  
• Fantastic Four by Jonathan Hickman, Vol. 4 (F4 #583-588)
  
• FF by Jonathan Hickman, Vol. 1 (FF #1-5)
  
• FF by Jonathan Hickman, Vol. 2 (FF #6-11)
  
• Fantastic Four by Jonathan Hickman, Vol. 5 (F4 #600-605)
  
• Fantastic Four by Jonathan Hickman, Vol. 6 (F4 #606-611)
  
• FF by Jonathan Hickman, Vol. 3 (FF #12-17)
  
• FF by Jonathan Hickman, Vol. 4 (FF #18-23)
  
  You can read straight up to F4 588, then FF 1 through 11, then: F4 600, FF 12, F4 601, FF 13, F4 602, FF 14, F4 603, FF 15, F4 604, FF 16, F4 605, F4 605.1, F4 606, FF 17-18, F4 607-608, FF 19-21, F4 609-610, FF 22, F4 611, FF 23.\
  
  Now, to step away from runs on the FF books proper, here's some mini-series and spin-offs worth reading:
  
  
• Fantastic Four: 1 2 3 4
  
• Fantastic Four: Unstable Molecules
  
• Fantastic Four: The World's Greatest Comics Magazine
  
• Fantastic Four: First Family
  
• Fantastic Four: Island of Death
  
• The Books of Doom
  
• Marvel Masterworks: Silver Surfer, Vol. 1
  
• Silver Surfer: Parable
  
• Silver Surfer: Requiem

Here's some stuff with MODOK you need to read:

• Super-Villain Team-Up: MODOK's 11
  
• Nextwave: Agents of HATE
  
• Secret Avengers by Ales Kot vol. 1
  
  For Spider-Man, check out the beginning of Dan Slott's current run, Spider-Man: Big Time. For the Fantastic Four, I recommend starting with Mark Waid's run: Fantastic Four by Waid & Wieringo Ultimate Collection vol. 1.
  
  I'd also recommend giving these a look:
  
  
• Immortal Iron Fist by Matt Fraction
  
• Daredevil by Mark Waid vol. 1
  
• Moon Knight by Warren Ellis vol. 1

IFanboy does lots of "Where do I Start?" bits for various comic characters/teams, they're usually spot on. Here's the link the F4 one: http://ifanboy.com/articles/fantastic-four-where-do-i-start/

Personally, I thought the golden age ones were sort of fun but not nessecarily "essential". The last on the list is Mark Waids run which just recently got an "ultimate collection" release, and is often really highly recommended (I just ordered the first 2 of 4 for myself) http://www.amazon.com/Fantastic-Four-Wieringo-Ultimate-Collection/dp/0785156550/ref=sr_1_1?ie=UTF8&qid=1370487644&sr=8-1&keywords=fantastic+four+waid

And Hickmans run also has rave reviews and will be released in omnibus form later this year (October), though it is available in smaller volumes right now as well http://www.amazon.com/Fantastic-Jonathan-Hickman-Omnibus-Volume/dp/0785165665/ref=sr_1_1?ie=UTF8&qid=1370487700&sr=8-1&keywords=fantastic+four+hickman+omnibus

I would add to this The Books of Doom, a recent origin story on Doctor Doom (though it doesn't feature the Fantastic Four, even though their name is in the title) http://www.amazon.com/Fantastic-Four-Books-Ed-Brubaker/dp/0785122710/ref=sr_1_1?ie=UTF8&qid=1370487776&sr=8-1&keywords=books+of+doom+brubaker

In that case, I'd say pick a character and start from the beginning of a "run" - meaning, a series of issues written by the same author. The best way to do this is via "trades" which are paperback books that collect a bunch of issues into one.

A few suggestions that I've personally enjoyed and are good to start with (with Amazon links to the first trade, but also, make sure you use your local library - either taking out physical copies or digitally via Hoopla):

Ultimate Spider-Man - Brian Michael Bendis

Fantastic Four - Waid / Wieringo

Gotham Central - Michael Brubaker

Daredevil - Mark Waid

Astonishing X-Men - Joss Whedon

Batman: Year One - Frank Miller

There are also tons of guides online, so if you have a specific character you want to start with, you can just google "best _____ comics to start with" and get some suggestions.

Don't be afraid to just jump in. Individual story lines for the most part can stand alone without any background.

EDIT: added the hyphen for the bot :)