Harry Potter stands at the very top of any plot of any book I've ever read. Following through on all the plot lines to satisfying conclusions, check. Embedding character "weaknesses" early on that serve as solutions later, check. Clashing character arcs (ie mini plot lines), check. Details that turn out to have massive importance (the whole series is encapsulated in book 1), check. Revelations that change the reader's view of "the truth," check. Irrevocable choices characters make that have good--and bad--consequences, check. The MC rising to the occasion after having to face worse than the worst he could imagine, check.
Other books that are excellent in plot:
The Scorpio Races, by Maggie Stiefvater--it is, hands down, one of the most structurally perfect books I can think of!
Flipped, Wendelin van Draanen--there is a lot of character and voice in this book, but it's also full of characters making choices that drive the plot. Also a very nifty solution at the end.
Alcatraz vs. the Evil Librarians (series) by Brandon Sanderson, for his setup of certain tools that the MC can use at the end to solve the problem
Al Capone Does My Shirts and the sequel, Al Capone Shines My Shoes, by Gennifer Choldenko--a really excellent example of the solution to book 1 setting up the problem for book 2
Things Not Seen, by Andrew Clements, for the way Bobby, the MC, takes charge of his fate and drives the plot
The Thief, Megan Whalen Turner--for using surprise elements effectively in the plot
Entwined, Heather Dixon--I don't know how else to describe the plot except to say it was sort of like chiasmus (a form of Hebrew and Greek poetry that is repeats itself in reverse, sort of like an hourglass). What you think is the "truth" at the beginning gets reversed over the course of the book, and the actions and discoveries the characters undergo.
The False Princess, Eilis O'Neill is also good for characters uncovering more information, which shifts your whole picture of what is really going on in the story.
Journey to the River Sea, Eva Ibbotson (a lot of her MG novels, actually)--there's a good deal of MG justice and characters getting what was coming to them, which has a lot to do with plot lines fully playing out
Rules, Cynthia Lord--a really great example of a contemporary novel with a really strong plot--each character has a strong arc, and a number of them clash with each other, and there are hard choices to be made that will create a very real outcome. Plot has to do with important choices your characters make that change things permanently.
Sorcery and Cecilia, or the Enchanted Chocolate Pot, by Patricia C. Wrede and Caroline Stevermer.
A Monster Calls, Patrick Ness--the parts just fit together really well, to the point that when it all comes together, it's like the story has snuck up behind you and walloped you over the head.
Cosmic, Frank Cottrell Boyce--for getting his impulsive character into a situation that only he can solve, but not without a GREAT number of problems. (Plus, it's funny! And heartwarming, too.)
How to Save a Life, Sara Zarr--again, a quieter contemporary novel that nevertheless has a plot, because people do things that strongly affect their futures as well as the futures of others.
The House of the Scorpion, Nancy Farmer
Brat Farrar, by Jacqueline Tey (an old mystery published as adult, but which I suspect would be marketed as YA today)--another good case of character arcs intersecting, plus a mystery
The Ghosts, by Antonia Barber--cool way all the plot parts fit together