A few for me that immediately come to mind...
Metroid
Best: It's difficult to say, but I'm actually going to go with Prime 2. The original Prime was fantastic, but there was a lot of backtracking involved, and very little direction. Echoes provided some much needed direction to your adventuring, a fantastic antagonist in the form of Dark Samus, and significantly less backtracking. The scenery wasn't quite as spectacular or memorable, but the bosses were a huge improvement, and the dark world mechanic was actually quite fun. It's been done to death in video games before this, but the impact it had on the light world encouraged me to explore everything, and the rapid loss of health gave me a sense of urgency whenever I was there. The soundtrack was also much better.
Worst: Other M. I don't really need to go into too much detail here...Other M is a sexist, poorly-written, poorly constructed pile of garbage that completely destroys Samus Aran's character, and I refuse to consider it a canon entry to the Metroid series. It takes the fantastic gameplay of the Prime series and the classic Metroidvania gameplay and turns them into something barely recognizable. In short, it does nothing right. The next Metroid game will make or break the series for me, because if this is a note of things to come...
Final Fantasy
Best: XII. One thing I have always hated about later Final Fantasy titles is the romance aspect. It's poorly written, robs the unfortunate female protagonist of what little personality she has before that, and it completely supplants the world-shaking events of the main plot. FFXII was everything I could have ever asked for in a 3D Final Fantasy: the world took precedence over the characters, the story was filled with political intrigue and sympathetic villains (I still consider Vayne more of a protagonist than the actual protagonists) and at no point was perspective lost. Vaan is a common complaint of FFXII, as he did absolutely nothing, but to me that didn't matter - the characters were of secondary importance to the plot, and it was more than engaging enough. No teenage angst? I can live with this. The battle system was a huge step up from previous titles - I loved tinkering with the Gambits - and, best of all, it slotted nicely into the rest of Ivalice's history. FFXII was a great part of something greater, and I enjoyed every second of it.
Worst: IX. Between XIII and IX, I'm going to have to go with IX, because it's unbearably boring. Coming off of VIII, which I adored, it felt like a giant step backwards. None of the characters really appealed to me, the battle system was unbearably slow - and it's aged terribly - and the world never really grabbed me in the same way that other titles did. FFXIII was truly diabolical, but it at least moved along at a steady pace, and became somewhat enjoyable once it opened up a little and let you explore Gran Pulse to your heart's content. FFIX, by contrast, remained tedious from start to finish. I had to force myself to finish it, and that is never a good sign.
Tales
Best: Symphonia. Symphonia was my all-time favourite game for the longest time, and it remains the best instalment in the Tales series in my opinion. No other Tales title has had such a fantastic cast, amazing villain - Tales games seem to shirk their villains quite a bit - or engaging world since. The battle systems have improved, but that's about it. Symphonia barely shows its age other than graphically now. It's a shame about the sequel though.
Worst: Abyss. God, I waited YEARS to play this game. It never came out on PS2 over here, so I didn't get to play it until the 3DS port came out. Either it's aged terribly, or it was never a very good game to begin with. The plot was uninspired and predictable, the cast was bland and unimaginative - with the exception of Jade, who had his moments - the villains were underdeveloped (which is unforgivable to me) and Luke...I just wanted to strangle Luke. Everything about him was poorly done. Vesperia had less direction, but it had a fairly good cast. Abyss had a poor cast and a dull story.
Disgaea
Best: Disgaea 4. The story of Disgaea 4 is a great one, filled with more subtle, political humour than the slapstick that marks other entries in the series. It's more mature, but it still has that Disgaea charm, marked by constant breaking of the fourth wall and utterly ridiculous statements that are said with complete and deadly seriousness. Valvatorez was such a great protagonist. The post-game is also the best so far. It's a CRAZY timesink.
Worst: Disgaea 2. This was awful coming off the second game! Barely any humour, a horrid story, and no significant upgrades in the gameplay. Every other Disgaea has brought something new to the tables. All this brought was a terrible cast of characters that have made for some horribly expensive DLC in future titles. It's not funny, it's not fun, and it's utterly forgettable. Definitely the black sheep of the family.
The Legend of Zelda
Best: Link's Awakening. I still love this title even now. For a Gameboy title it's impressively large, and whilst I'm picking it primarily for the nostalgia value, no other Zelda game has been so enjoyable to me every time I've picked it up and replayed it. Marin makes a much better love interest than Zelda does any day of the week. Being electrocuted for stealing and then being referred to as "THIEF" by everyone never got old either. xD
Worst: Skyward Sword, for two reasons. One is the world, which isn't so much a world as it is a series of tiny areas you hop to and from. Skyward Sword is TINY even by Zelda standards, and extremely disappointing in its lack of originality. The second reason is the motion controls. Don't get me wrong; swinging the Wiimote to swing your sword is awesome. It felt right, it felt good, and it made combat so much more entertaining and enjoyable. It's the one good thing about this game. No, the problem lies in everything else. Wave your Wiimote to control your bird. Tilt your Wiimote to control your angle of descent. Shake your Wiimote to shake things off. Point your Wiimote and have it act like a compass needle. None of this worked. It was excessive. Exhausting. Poorly handled and it made controlling the game outside of combat a chore and a nightmare.
Castlevania
Best: Portrait of Ruin. What made this memorable were the boss battles. Stella and Loretta, as annoying as they were, opened up the game and made it amazing. Purify them and you then get to fight Brauner. Beat him and then you go on to fight Dracula and Death. At the same time. That fight is the highlight of the entire franchise for me: two of Castlevania's staple bosses, typically the hardest ones, in a room, together. One throwing fireballs, the other throwing scythes. Teaming up for combo attacks, just as you have for the whole game. Priceless.
Worst: Dawn of Sorrow. Aria of Sorrow was a great game...its sequel, not so much. The symbol-drawing was ridiculously contrived and highly aggravating, the villains were throwaway at best, and it felt like a half-arsed, cobbled-together sequel just for the sake of having a Castlevania title on the DS. Disappointing.
Atelier
Best: Meruru. A lot of people say Totori is better, but I disagree. Meruru was a hugely likeable protagonist, and it's great watching her evolve over the course of the game from a spoiled Princess to one who genuinely cares about her people. The cast returning from Rorona and Totori have matured and gotten much better as characters, having the history of two games behind them, and the exchanges are light-hearted and often quite funny. Watching the overworld map evolve as you develop the kingdom is a fantastic mechanic to track progress, and the battle system and alchemy systems reach their peak here as well. The soundtrack is also much better, and the endings more satisfying. As good as Ayesha and Totori are, neither have Meruru's scope.
Worst: Rorona. Rorona Plus mercifully fixed a lot of the problems Rorona had, but it doesn't change the fact that it's the weakest instalment in the Arland trilogy, and one of the weaker ones in the franchise as a whole. Rorona and Sterk just can't carry the game by themselves, and there aren't many memorable characters otherwise. They go on to be memorable in later titles, but in this game, even in the Plus version, they're severely lacking.
...there are more I could go into, but I'm tired of writing at the moment. xD