Here's the best cards in the game, by set, and why.
 
Base Set
5. Blastoise - It's raindance is where this card shines. Get him out as early as possible, and, with the help of a Professor Oak, just load your energy on your Articuno, Gyarados, or even himself.
4. Professor Oak - The most powerful card drawing tool in the game. When you have a crappy hand, a small hand, or no hand, use this to get you back on track. Play it wisely though. Don't deck yourself.
3. Bill - The most versatile card in the game. This is the only card where you can say that is useful in any given situation. Put 4 of these in your deck.
2. Electabuzz - With 2 energy, he averages 35 damage, and 5 to himself. Plaus, he has a one-energy attack. Good HP, and huge power makes this guy one of the best.
1.Hitmonchan - This guy is pure speed. Good HP, and sheer quickness, makes this guy so devestating. Stick one fighting energy on him, and let him jab away, as you charge up your bench, to get ready for a new wave of beating for your opponent.
Honorable Mentions: Chansey, Computer Search, (super) Energy Removal
 
Jungle Expansion
5. Vileplume - His HP is pathetic, and his pokemon power isn't so great either, but his petal dance is amazingly powerful. With an average of 60 damage, just retreat or switch, and get him back out for more whippin. Good with Venusaur too.
4.Jigglypuff - Pretty good HP. Lullaby and pound are very dependable. Possibly the bes psychic hoser. Resistant to psychic, and does exactly 20 damage, which is small enough to get through the invisible wall.
3. Kangaskhan - An awesome staller, and an even better card drawing tool. Slap one energy on him, fetch away, as you load up your bench with energy, and get ready to attack. Don't bother with comet punch.
2. Mr. Mime - The most defensive pokemon in the game. With the use of an Alakazam and a Chansey, this guy can be unstoppable. Also, he's got a good attack as well.
1. Scyther - The most versatile and arguably the best pokemon in the game. 70HP, free retreat, and a good attack that could be done with any energy. Also, resistance to fighting, which is the most widely used color type, in the game. Consider him a colorless pokemon, with a bonus, because nothing is weak to fighting, but a few cards are weak to grass. Also, you got another bonus if you play grass in your deck, with sword dance. dance and gust. Sweet!
Honorable Mentions: Wigglytuff, Exeggutor, Clefable
 
Fossil Expansion
5. Gengar - If you can find a good use for this card in a new deck, this card can cause serious damage to your opponent. Throw the damage from your opponent's pokemon any way you like. It's like a constant pluspower. It's attack is pretty sweet too. Best of all, it evolves from a good basic pokemon and an awesome Level 1. Too bad it's a Level 2 evolution card. Ouch.
4. Haunter - No weakness. Resistant to fighting. Free Retreat. Dodges half of the opponents attacks. Attack that sends the opponet to sleep. Could you aske for more defense from a Level 1 pokemon? There is a reason why this card is a rare card, instead of an uncommon.
3. Lapras - Another awesome card for the raindance. He's got awesome HP, and his water gun is better than it looks. attack on 3 consecutive turns from the start, each one being progressively more powerful. Confusion can save you the game in emergency situations. The Raindance just got that much stronger.
2. Articuno - Here's an old question that dated back when only base set existed. What should i use as an attacker for my raindance deck? Dewgong, or Gyarados? The correct answer is Articuno. Basic Pokemon. 2 Devestating attacks. Resistant to fighting. Good HP. You can't ask for more.
1. Ditto - This card basically has no weakness. He's just as good as the opponent's pokemon, and then some. He can feed off any energy, and you can benefit off of your opponent's hard work of evolving his pokemon. One bad thing is, he can die in so many stupid ways, but nonetheless, his positives exceed his negatives, big time.
Honorable Mentions: Magmar, Energy Search, Hitmonlee
 
Movie Promo Cards
Mewtwo - The only good card out of the four. It can potentially do 40 damage on it's second turn out. Just have a way of putting energy in your discard pile. Here's some ideas: Pokemon Center, SER, Scoop Up, Computer Search, Professor Oak, Retreat, Die (some tip, eh?), many many more.
 
btw, the rest of the promo cards suck.