Some combinations of cards have proven to be highly effective, yet versatile enough to be used in several different decks.
The numbers provided are typical counts, but are not set in stone.
4 Holon Transceiver
2 Holon Mentor
1 Holon Adventurer
1 Holon Scientist
The Holon Engine provides a lot of versatility, due to Holon Transceiver acting as extra copies of any of its Supporters.
Suppose you're using Holon Mentor on Turn 1/2 to set up. Compare that to, say, Lanette's Net Search. You can only have 4 copies of Lanette's Net Search in your deck, but you can have an effective 6 copies of Holon Mentor, due to Holon Transceiver being able to search for and play Mentor in one turn.
The advantages don't end there. Later in the game, Lanette's Net Search may be a dead draw because you already have all the Basics you need. Holon Transceiver will not be — you can simply use it to get Holon Adventurer or Holon Scientist instead of Holon Mentor.
At least 2 Mentor is the norm, due to how valuable it is early-game, and how devastating it can be to play only 1 copy in your deck and have it Prized. Decks that rely on Holon's Pokémon as Energy will play more copies.
Other Holon Supporters (Holon Researcher, Holon Farmer, Holon Lass) can be added to the Holon Engine if your deck requires them.
You generally do not want to play Holon Transceiver if you've already played (or are going to play) another Supporter for the turn, as you can't play the Holon Supporter that you search for immediately, and you can Transceiver into Supporter next turn instead. Delaying Transceiver until necessary also defends against Rocket's Admin., as not playing Transceiver means it's an additional hit in your deck if they decide to Admin you.
The exception is when playing against Trainer locks, like Manectric ex. Against those decks, not playing Transceiver could mean that they evolve and Disconnect you after you pass the turn, leaving you with a dead Transceiver in hand. If you had played the Transceiver, you'd have a live Supporter instead.
2 Jirachi
2 Pidgey
1 Pidgeotto
2 Pidgeot
4 Rare Candy
A common core in Stage 2 decks, wherein Rare Candy serves as an accelerant and a "wildcard Stage 1" to evolve into Pidgeot or the main attacker/engine Pokémon.
The Holon Engine is a common accompaniment, as it can find Jirachi, Pidgey, and either the Basic form of the attacker, or Holon's Magnemite/Voltorb to retreat the starting Pokémon into Jirachi. Once Jirachi is active, it will use Wishing Star to dig for missing pieces such as Rare Candy (Pidgeot can be searched for with Supporters). After getting Pidgeot onto the field, setup accelerates even further, as Pidgeot's Quick Search can be used even when it's not Active, and it lets you see your entire deck, not just the top 5 cards.
If the rest of the deck consists of mainly δ Pokémon, Holon's Castform can be played instead of (or in addition to) Jirachi. Instead of looking through 5 cards with Jirachi's Wishing Star, you straight up draw a comparable number of cards with Castform's Delta Draw.
This core is disrupted by anything that stops Poké-Powers. Cessation Crystal is the most splashable option for that. Girafarig will stop Jirachi, and Battle Frontier or Solrock's Luna Shade will stop Pidgeot.
3-4 Castaway
3-4 Cessation Crystal
0-2 Balloon Berry/Fluffy Berry
0-2 Lanette's Net Search/Pokémon Fan Club
Castaway can be used as the first Supporter of the game, searching up Lanette's Net Search or Pokémon Fan Club to get Basics next turn, as well as a basic Energy and a Pokémon Tool for value. Two common Tools to get are Cessation Crystal if your starting Pokémon can make use of it, or Balloon Berry/Fluffy Berry to retreat into another Pokémon that you'll play next turn off Lanette/Fan Club.
Later in the game, Castaway can search for another copy of itself, providing a constant stream of Cessation Crystals to replace those that get removed.
This package lets you get away with less than 4, usually 2, copies of Lanette's Net Search/Pokémon Fan Club, much like the Holon Engine. However, since you have to play Castaway and the Basic searchers on separate turns, it can be a little slow and susceptible to disruption from Rocket's Admin. or Stantler's Push Away, especially if you go first and your opponent has two turns to attack before you play the Basic searcher. Some decks don't play Basic-searching Supporters with Castaway, but the ones that do usually have high HP Basics, such as Stantler, Rayquaza ex δ, or Latios ex δ, that can avoid getting donked (losing their only Basic Pokémon, and hence the game, very early to a swift attack).
2 Voltorb
2 Electrode ex
4 Pow! Hand Extension
Electrode ex's Extra Energy Bomb leaves you down two Prizes, but to borrow a saying from Magic, the only Prize that matters is the last. In exchange for KOing itself, Electrode ex accelerates your Energy attachment and turns on Pow! Hand Extension, allowing you to mount a strong comeback. Rocket's Admin. would be the perfect ender to this combo, forcing your opponent into a low hand size after they've taken 2 Prizes.
The beauty of Pow is that if you are already down in Prizes, it can force Cessation Crystal-equipped Pokémon (as well as Pokémon with Power-blocking Bodies, like Muk ex) out of the Active Spot, giving you a window to use Extra Energy Bomb.
Jirachi ex and Sceptile ex δ stop Extra Energy Bomb in ways that cannot be disabled by Pow.
2-4 Windstorm
0-2 Warp Point
This package is commonly used in decks that need answers to anti-Poké-Power cards.
Windstorm removes Cessation Crystal or Cursed Stone. Warp Point deactivates Cessation Crystal by forcing the equipped Defending Pokémon out of the Active Spot. The opponent can have 2 Cessation Crystal-equipped Pokémon to play around it, but this tactic loses to Windstorm removing both of them.
The Windstorm count can go up if you don't have Stadiums of your own to remove opposing Cursed Stones, and vice versa. You usually don't want too many Warp Points, as when you're trading hits with your opponent, Warp Point may allow them to switch their damaged attacker for a "Substitute" Basic. If you can't spread damage to their Bench, you'll have to attack into and KO that Basic, letting them promote their attacker and get one more hit in with it.
Electrode ex decks can cut Warp Point, as they have Pow.
1 Girafarig
1 Lunatone + 1 Solrock OR 3 Battle Frontier
This package consists of cards that shut off Jirachi and Pidgeot. Usually played in decks whose main attackers are Pokémon-ex (and thus cannot equip Cessation Crystal), and are not playing Jirachi + Pidgeot themselves.
The Holon Engine is also commonly used, as Lunatone + Solrock is a 2-card combo.
Space Center counters all of these cards. You can use Desert Ruins to go after the Pokémon-ex that these cards are typically played with instead, unless your Jirachi + Pidgeot deck also uses ex's.
The diagram to the left shows how various packages mentioned so far interact with each other.
Green boxes ▢ indicate cards that are played together.
Red arrows X → Y indicate that card X is countered/punished by card Y.
4 Copycat
4 Professor Oak's Research
4-6 Master Ball/Poké Ball
These Trainers form the backbone of a few builds that only play a single 4-4 Evolution line, e.g. Arcanine ex, Manectric ex, Scizor ex. These decks play a lot of Item cards (the Balls, and also Energy Removal 2/Pokémon Reversal, which we'll see later), so they can empty their hands and refill it with Supporters every turn. They don't play Evolution-searching Supporters; their preferred method is to use raw draw power and spam Balls. With 4 copies of the Stage 1 and only one Evolution line, they have better chances than other decks of topdecking the right Evolution off a draw spell, and if they draw into a Ball instead, they can cash it in immediately for another spin on the wheel.
Copycat, and the ubiquitous Rocket's Admin., work well in the early-game, especially if you mulliganed (a common occurrence, due to only playing 4 Basics: ~60% of your 7-card hands are mulligans). Copycat matches your opponent's cards in hand, whereas Admin neutralizes their advantage. Professor Oak's Research is more reliable late-game.
3 Dunsparce
4 Swoop! Teleporter
Some decks use Dunsparce's Strike and Run to set up. Since it costs Energy, starting with Dunsparce Active is ideal, as you won't have to spend an Energy attachment retreating into it and another Energy attachment powering up Strike and Run. Swoop! Teleporter acts as redundancy, letting you swap your Active for Dunsparce. Later in the game, it can thin your deck by Swooping away worthless Dunsparces.
You can apply the same principle and play Swoop with other Basics that setup with attacks, like Holon's Castform or Paras. Sometimes Tauros takes the place of a Dunsparce. You can't Swoop an ex away, so decks with Basic ex's might want to look for other setup options.
In terms of consistency, your typical Holon Engine + 2 Jirachi deck has 8 ideal starters (4 Transceiver, 2 Mentor, 2 Jirachi). 3 Dunsparce + 4 Swoop is 7, which is less, but the fact that you're running 3 Dunsparce instead of 2 Jirachi means you're slightly more likely to naturally start Dunsparce after factoring in mulligans.
1 Mew ☆ δ
2 Warp Energy
1 Holon's Castform/Electrode/Magneton
This package is meant to beat lock decks. Warp Energy counters Pow! Hand Extension, a lock deck staple. Holon's Pokémon lets you reuse attached Warp Energy, and fixes colors if you need to attack with Mew ☆ δ. Against specific decks...
Rayler: Mew ☆ δ can copy Rayquaza ex δ's Special Circuit to spread damage and stay even on Prizes. Both sides take the same number of hits (3) to KO, but the Mew side is advantaged as Mew only gives up one Prize.
Camler: Mew ☆ δ can copy Camerupt's Back Burner to get back (basic) Energy that was discarded by Numel's Kindle or Energy Removal 2. It also hits Camerupt for Weakness.
Rat Lock: Mew ☆ δ can copy Raticate's Pickup to avoid running out of resources.
2 Minun OR 2 Rattata + 1 Raticate
2 Mr. Briney's Compassion
Sniff Out or Pickup can be used to loop Mr. Briney's Compassion endlessly. The basic setup is a Minun with an Energy on it Active, another Minun Benched, and one copy of Mr. Briney's Compassion each in your hand and discard pile. First you play Briney from hand on the Active Minun, then promote the Benched Minun, attach Energy to it, Bench the Minun that you Briney-ed to hand, and finally use Sniff Out to get back the Briney in the discard. This leaves you right back where you started, with all damage on the Active Minun wiped.
This loop can be broken if your opponent can do enough damage to KO Minun in one hit. It can also be disrupted by them playing Rocket's Admin. and you whiffing Briney on the redraw.
1 Celebi ex
1 Pidgeot P2 (in addition to the Pidgeot RG line you're already playing)
2 Warp Energy
This combo lets you recycle cards from your discard pile endlessly. The basic setup is a Pidgeot Active and a Celebi ex in hand. Play Celebi ex onto the Bench and use Time Reversal to recycle a card, then use Pidgeot's Beating Wings to shuffle Celebi ex into the deck. You can repeat this when you search/draw into Celebi ex again.
Warp Energy helps get Pidgeot into the Active Spot so it can use Beating Wings. It can retreat for free after it's done.
4 Energy Removal 2
4 Pokémon Reversal
A simple combination of full playsets of two powerful, but luck-reliant effects. Generally played in fast, aggressive decks that seek to capitalize on slow starts, said starts either arising from unlucky draws from the opponent, or lucky flips on these two cards.