Ok.
Basic:
This took some thinking, but after awhile I came to the conclusion that Uxie must be the best basic. It's played in nearly every competitive deck; for good reason.
It has the element of dropping from your hand, and allowing you to refresh your options, and then boomeranging back into the deck for a measly colorless energy. It's Psychic typing allows it to hit some contenders fairly hard, such as Machamp, and is optional, so you can allow Uxie LA to absorb damage then pop it back in your deck. The only downfall is the constant threat of Power Spray from SP decks, and the low HP.
Stage 1: Clearly, this is a no-brainer, Claydol GE, the most important card for any deck that doesn't run 2 Uxies. It's a Stage 1, which is a hassle, but the pain of evolving it is EASILY overcome by the great asset it is to any deck, the ability to put junk cards from your hand to the bottom of your deck and then draw up to an amount of 6 depending on your current hand is unbelievably important for any consistent deck, I know people that run 2-3 Claydol just for consistency.
Stage 2: This one isn't so black and white, as there are many great (and some not so great) stage 2's; Gengar SF is an obvious pick for some, but it's lack of genuine hard hitting damage is disappointing, and in reality it is based purely on luck. Machamp SF is just the cheap and easy way of playing, and Flygon RR was over hyped but was a good card nonetheless. If I had to choose personally it would be Ampharos (Great) from the Heart Gold Soul Silver set,
#34 - (Great) Ampharos - Lightning - 140 HP
Stage 2 Evolution - Evolves from Flaaffy
Poke-Body: Conductivity
Whenever your opponent attaches an Energy card from his or her hand to a Pokemon, place 1 damage counter on that Pokemon.
[L][C][C] Lightning Crush: 40 damage. Flip a coin, if heads this attack does an additional 40 damage. If tails, discard 1 Energy attached to the Defending Pokemon.
Weakness: Fighting (x2)
Resistance: Steel (-20)
Retreat: 2
Mainly due to the fact that it essentially kills Feraligatr great, who I understand is weak to grass, but in the fact that Ampharos' PokeBody harms any Pokemon that Feraligatr tries to overpower by a great sum if they try to go for a big attack, particularly Water Crunch
[W][W][W][W] Hydro Crunch: Does 60 damage plus an additional 10 damage times the number of damage counters on the Defending Pokemon.
Level X: Luxray GL. 'nuf said.