For instance, my favorite book out of the Riddle-Master trilogy is Heir of Sea and Fire (by Patricia McKillip). I don't necessarily think it is the best written of the three books, I just like it the most what with the main characters seeking revenge, yet neither precisely sure who they are seeking revenge from or on. I feel the same way about Chamber of Secrets by J.K. Rowlings, which I've always been very fond of. It has the strongest horror (as in genre, not as in lots of people croaking) of all of her books; I'm also convinced that it was originally supposed to be the first book or was combined with the first book and then her editor said, "Hey, you know you could turn this entire plot into a separate book." It feels introductory.
There are those sequels I've grown to love over time. When I was a kid, I didn't care for The Voyage of the Dawn Treader; now it is one of my favorite Narnia books. The same is true of Perelandra, also by C.S. Lewis. It is just so heavy content-wise and exposition-wise, I couldn't get through it. I have since, and I like the book, although I still think Out of the Silent Planet is the best of the three. All in all, I don't think Lewis' sci-fi has ever received the credit it deserves. He was writing in the age of Asimov; now, I admire Asimov tremendously, but I also admire the sci-fi writers who have concentrated more on people and societies than machines and systems (although someone like Cherryh does both effortlessly). Anyway, Lewis was one of the first to write sci-fi that was about "first contact," as Star Trek would call it, rather than about tech/robot/alien wars. (Although to be honest, I think I just love Out of the Silent Planet for the part where the bad guy, Weston, is blathering on with his academese and pompous references to "Life As She Is Lived" and Ransom, who is trying to translate Weston's long-winded speech, gets confused and says, "I'm sorry, I forgot who She is.")
Back to sequels, Madeline L'Engle wrote somewhere that the first book you write is always the best because it is the one you really wanted to write. That might be true. When it comes to mystery series, however, I have found that nearly always (with exceptions) the latter books are better than the first, or, at least, more grounded. The author knows her characters better, her milieu, her detective's history. I much prefer Christie's later Poirot books to her first; I enjoy Crocodile on the Sandbank (first Amelia Peabody) by Elizabeth Peters, but it has an incredibly convoluted plot (although actually, most of Peters' books have convoluted plots). Mystery writing is evidently a craft that has to be practiced to be learned. Unfortunately, once it is learned, it quickly becomes trite so mystery series follow a kind of bell curve: okay first novels with convoluted plots, better sequels, a peak and then a falling off where every book is just a repeat of the one before.
Speaking of series, Steve Hockensmith recently wrote a book called Holmes on the Range, a Sherlock Holmes inspired mystery. The main character is not Holmes; he is a cowboy whose younger brother (his Watson) reads him newspaper stories about Holmes. The cowboy becomes convinced, with reason, that he has the abilities, if not the book learning, to emulate Holmes and sets out to prove so. It is fantastic, and I am hoping it is the first of many.
Returning to sci-fi, and fantasy, I prefer Ender's Game to its sequels, which lost a little of the magic, I think. Also, Fellowship of the Ring is my favorite of Tolkien's trilogy; I have read it more than the remaining two books. I'm not sure why. I don't think Tolkien knew where he was going in Fellowship, and it's a little uneven as a result, but I prefer both the book and the movie. I think part of it is the wrenching one feels when the story ends in book 3, a wrenching, I'm happy to say, Jackson (with the help of Annie Lennox) did invoke from me at the end of Return of the King. There are two solutions to great quest stories: Lewis' solution was transcendence; Tolkien's solution was loss. Either way, one cannot return to the status quo and either way, something will change. So, the ending of Lord of the Rings must be sad. But being sad on a regular readerly basis is asking rather a lot.
Turning to good sci-fi/fantasy sequels, I include Diane Duane's Deep Wizardry (#2), Chernevog by C.J. Cherryh (#2: Rusalka is the first); Asimov's The Naked Sun (#2: Caves of Steel is #1); Douglas Adams' Long Dark Tea Time for the Soul (sequel to Dick Gentley's Holistic Detective Agency, both great and less well-known than Adams' Hitchhiker's series); Queen of Attolia and King of Attolia by Megan Whalen Turner (books #2 and #3: #1 is The Thief; I LOVE this series); The Lives of Christopher Chant by Diana Wynne Jones (prequel to Charmed Life, also good); not sci-fi or fantasy: Ashes to Ashes by Emma Lathen (my favorite of that mystery series); Parting Breath by Catherine Aird, my favorite of that mystery series; the latest P.N. Elrod, Song in the Dark (vampire/mystery series), more thoughtful, less gorey than its predecessors; The Finer Points of Sausage Dogs by Alexander McCall Smith (#2 of a 3-book series), which is absolutely hilarious; and finally, Jonathan Strange & Mr. Norrell by Susanna Clarke--not really a series, but I've seen it split into three books, I highly recommend it all.
Disappointing sequels (not necessarily sci-fi/fantasy): Murdering Ministers by Alan Benchley (his first, An Embarrassment of Corpses is hilarious; his second is just tedious; I guess L'Engle was right!); the last Sarah Caudwell book The Sibyl in her Grave which is, in fact, very good but depressing without the panache of the others; The Gypsy Game, sequel to The Egypt Game by Z.K. Snyder, written many years later; it does not stand up to the comparison; McKinley's Rose Daughter, her re-retelling of Beauty and the Beast; she did it already with Beauty; why do it again? The last few books in Susan Cooper's Dark Is Rising series. She didn't go for transcendence or loss--series ended with a thud.