Here you'll see the basics for deck-building, they may sound a bit strange, but I'm an advanced player and I promise that a deck made according to these rules will be a good deck (most of the time).

Starting Off
first you start with a strategy, if you think you have a perfect strategy, then you're ready to start.

The Basics
What a deck should look like:
15->20 Pokémon (18 is recommended)
15->20 Energies (16 is recommended)
minimum 20 Trainers

20 is really the maximum, only if your deck is based on energies/pokémon or if there's really no other way.

What To Add
Pokémon:
Well, you almost always need a starter pokémon, a Pokemon that starts while charging your other Pokémon. If this Pokémon is one of the basics of your evolved Pokémon, then you're lucky, otherwise, you need others. Try to think a lot about a strategy and try to make it perfect, your main Pokémon line(s) are the most important, make sure you can have a quick setup.
If you use stage1, have the same amount of stage1 as basics (if there are more then 1 stage1 possible, use a maximum of 6). If you use stage 2, use 1-1-1 / 2-1-2 / 3-2-3 or 4-3-4 lines together with rare candy. Don't use more then 3 stage 2 lines (2 is best) 
most used starters:
Plusle DX
Jirachi DX
Unowns UF
Wobbufet HP
Corsola UF
Absol LM
Holon's Castform HP
Tauros CG
Luvdisc CG
Lickitung DF
Yanma UF
...

Trainers:
well, search and draw trainers for sure, stadiums if needed or to counter other stadiums. other trainers, sometimes if needed
like this:
4->10 draw cards
4->12 search cards
0->6 stadiums
0->12 other trainers

Search Trainers:
Prof. Elm's Training Method for evolved ex deck
Celio's Network for non-ex decks
Holon Mentor for basics (-ex) decks with less then 100HP
Holon Fossil for fossil decks
Great Ball for basic non-ex decks
Wally's Training for Turn1 decks (there are better cards for T1 decks)
Dual Ball for basic ex decks
Scott for stadium based decks
Holon Transceiver for decks with a lot of holon supporters, 4 of these and a lot of holon supporters is called a holon engine
Castaway for tool cards using decks
Holon scientist for delta decks

Draw Trainers:
Mary's request for non-stage2 decks
TV reporter for decks based on cards in the discard pile
Bill's Maintenance for decks with form change/forecast/shuffle decks.
Fieldworker for breakdown decks
Holon Adventurer for delta decks
Island Hermit for almost all decks, but it can be useful in decks that are based around a pokémon*
Holon Scientist for decks with a holon engine as an extra card, it can go in any deck
Professor Cozmo's Discovery For almost any deck as a regular draw card
Professor Birch Not really useful, but it can be used in a deck that requires you to use a lot of cards from your hand
Copycat for every deck, ton save you from a bad start

Stadiums:
Holon Research Tower, Holon Lake and Holon Ruins for delta decks
Giant stump and Cursed Stone for annoying decks
Battle Frontier, crystal beach and Space Center for disturbing decks
Pokémon Park for healing decks
Low Pressure System and High Pressure System for type-based decks
Strange cave for fossil decks
Full Flame for burn decks
Holon Circle for stall decks
Holon Legacy for delta decks without powers or for disturbing decks
Pokémon Park and Meteor Falls are alternative, there isn't really a specific kind of deck to use them in

Others:
well, I can't say much about these trainers, cause there are so many, play with what you like/need, that's all I can say. A lot of these cards are essential for your strategy, so they're worth taking a look at. Adding a couple of Tool cards to your deck can never hurt.

Energies:
very necessary, not only to charge, but also for special effects:

when???
basic, depending on the type you need
Dark/metal, only when needed (duh)
holon, depending on the effect and your type of basic energies
scramble, depending on your energies needed and the HP of your Pokémon
double rainbow, only for Turn1 decks or quick charge decks
React, only when you need it
multi, well, only when you really need it
rainbow, only in many type decks or dark/metal decks
d rainbow, only for delta decks (duh)
boost, only for Turn1 decks or energy based decks
dark metal, only for dark and/or metal decks
cyclone, only for annoying decks
warp, only for switch decks

Holon's Magnemite, Magneton, Voltorb, Electrode and Castform can be used as Energies, but be careful with magnemite, voltorb and castform because they are basics, and this means that if they are the only cards in your start hand you have to play it, a giant advantage of using these cards is that they are pokemons in your discard pile, deck and hand.