For Red/Blue, I'd say the top 5 are Nidoran-M, Nidoran-F, Squirtle, Abra and Zapdos.
The Nidoran have great availability, can evolve into their final stages very early in the game and don't require many high demand TMs.
Squirtle takes longer to evolve and really likes to have the Dig and Ice Beam TMs, but other than that it has the same advantages.
Kadabra is extremely strong and can hold the entire together on his own. Even if you don't evolve him into Alakazam he is one of the strongest Pokemon in the game. The only disadvantages here are the difficulty to catch Abra and the effort it takes to baby him up to level 16. There are no Elemental Punch TMs in this game to help with that.
Zapdos can carry you through the rest of the game once you catch it, its only problem is that you can't catch it before Koga. By this time most of the game is already done and there are very few difficult fights left.
Honorable mentions to Articuno, Jynx and Farfetch'd.
Articuno is mostly just a slightly worse Zapdos. If you think the difficulty and catching and raising an Abra is too much to put him in the list, Articuno should probably replace him.
Jynx is one of the best Pokemon I used in this game. Ice and Psychic are by far the best two STAB moves to have at this point, being Super Effective against 5 of the remaining 8 Gym Leaders/E4 members, and having a massive advantage against Sabrina as well. Jynx also gets Lovely Kiss for the few Pokemon she can't OHKO and the experience bonus from being a traded Pokemon. Jynx requires the Psychic TM, though there really isn't much else to give it to, and likes the Ice Beam or Blizzard TMs, though Ice Punch is strong enough to last the game. Jynx's one disadvantage is how late you get her. You get her at almost the same point as Zapdos and Articuno, who are both clearly better than Jynx though still more difficult to catch.
Farfetch'd is the best utility Pokemon in the game. Only Pokemon to learn Fly and a second HM (Cut) in the game and you get him just in time to use Cut. Even in battles Farfetch'd is a contender for the best Normal/Flying Pokemon, thanks to its trade experience bonus, Sand Attack, Swords Dance and Slash. Still not top 5, but definitely the most underrated Pokemon in the game.
Worst five I'm not too sure on. I haven't used most of the crapmons yet, so I can't give a solid opinion.
Ditto is definitely one of them though. He is actually not as bad as people make him out to be. The AI is garbage in this game and the movesets are even worse. Most Gym Pokemon only have one move that actually does good damage against themselves and they usually don't pick it. Ditto can nearly always beat one or two Gym Leader Pokemon by itself. Still, it is really difficult to train and you will still always have better options available against the Gyms.