Things you'll need to go from Generation 3 --> 6 (aside from games)

• Nintendo DS, or Nintendo DS Lite (contains both a GameBoy Advance game pak slot, and a Nintendo DS game card slot)
• A Second Nintendo DS to transfer Pokemon from generation 4 --> 5
• A Nintendo 3DS to transfer Pokemon from generation 5 --> 6. If you have a 3DS, you don't need the DS from the last step.

Generation 3 --> 4

Transfer up Pokemon using PalPark from Ruby, Sapphire, FireRed, LeafGreen, and/or Emerald to Diamond, Pearl, and/or Platinum. For this you need an original Nintendo DS or a Nintendo DS Lite as you need access to a Nintendo DS game card slot, and a GameBoy Advance game pak slot. Additionally, you can not transfer up eggs.

Gamecube Games --> Gen 3

You can also transfer up Pokemon from Pokemon Colosseum or Pokemon XD: Gale of Darkness to a modern Pokemon game, you just need to transfer them via trade to a generation 3 game, and then transfer them up like normal Pokemon.

Generation 4 --> 5

At Route 15 in Black or White you'll have to transfer everything up from your generation 4 games. For this, you'll need 2 Nintendo DS systems, one following the instructions in Pokemon Black, White, Black 2, and White 2, and another with the generation 4 game inserted running DS Download Play. You can transfer up Pokemon in this fashion, however there are a few stipulations:

• Held items will not be transferred up to generation 5 (they'll automatically be returned to the player's bag)
• The Pokemon being transferred can not know any HM moves.
• You can not transfer eggs.
• The Spikey-eared Pichu (a promotional exclusive) can not be transferred up.

Generation 5 --> 6

Starting December 27th 2013, download the 3DS application titled Pokemon Bank from the Nintendo eShop. This application can take Pokemon from a Generation 5 or 6 Game, and store them inside of the app. After this process is done, withdraw the Pokemon from Pokemon Bank in your generation 6 game.

Things to note when transferring Pokemon

• All Pokemon are forever lost from their past generation game - there is no way to transfer a Pokemon back to its previous generation.
• Game mechanics change between generations. While a team might be effective in one game, it might not prove to be useful in another. Notably moves are assigned physical or special in generation 4 onwards; and generation 6 introduces new mechanics such as the fairy type, base stat changes, and move changes.

No. Let's break this down a little:

• To get Pokemon onto X/Y (Gen6), you need one of B/W/B2/W2 (Gen5)
• To get Pokemon onto B/W/B2/W2 (Gen5), you need two DS units, one of them with a Gen4 game (D/P/Pt/HG/SS).
• To get Pokemon onto D/P/Pt/HG/SS (Gen4), you need a Gen3 (R/S/E/FR/LG) GBA cart inserted into the bottom slot of a DS/DSlite.

At no point along these steps is there a legitimate means to transfer Pokemon from a ROM on your PC to the official game cartridges.