Currently Online 
This was the year with lot of mixed feelings for me.
Gothic became fully open world with Gothic 3, as well as open ended, and while I appreciated that and found it very fun to play, due to time constraints and pressure from the publisher, it launched way too early (with around year more of work to do according to devs), full of bugs and nowhere near the polish, care and attention to details of previous 2 installments.
Oblivion looked great, and it was fun to play for a while, but it was painfully obvious that Bethesda was slowly, but surely dumbing down TES for mass market (culminating in Skyrim).
Twilight Princess had fantastic dungeons and I really liked world and Midna as companion, but its overworld was still lackluster compared to 2D Zeldas of the past and it was obvious that Aonuma didn't want to change the formula.
There were few pleasant surprises - Dark Messiah of Might and Magic was first person melee game, and although I was hoping for second Arcane's game to be more like their first, Arx Fatalis, Dark Messiah was so fun I was instantly hooked.
Dreamfall: Longest Journey was brave attempt at changing how adventure games look and feel, switching to 3rd person perspective of action-adventures, instead of usual point & click. It was not as good as Longest Journey, but still very good.
I didn't play Okami until few years later on Wii, and really enjoyed it. Not sure I ever seen Zelda connection in that one (unlike in Darksiders), but great game on its own.
Prey and Call of Juarez were FPS games of that year for me. Call of Juarez for its western setting and Prey for its us of portals, variable gravity and ability to detach your spirit from body and roam for a short time with limited ability to interact with environment (thus solving some puzzles) or attack enemy.
Dwarf Fortress also launched in 2006.
"Before playing, the player has to set in motion a process which generates a fantasy world with continents, oceans, and islands, produced via generative geology and hydrogeology, meteorology, and biogeography, and then simulates the evolution of all civilizations down to the lives of their inhabitants in order to yield a coherent world with internally consistent lore and history. The main game mode, Dwarf Fortress mode, is a colony management game that starts with selecting a suitable site from the generated world, establishing a successful colony or fortress, combating threats like goblin invasions, monster sieges, or undead hordes, generating economic wealth and taking care of the dwarves. Each creature, from animal to dwarf, is modeled down to its body parts, bodily fluids, organs, bones, teeth, hair, and tissues (which, depending on the creature, can be made of more unusual fantastic materials such as metal or stone, or even mist, fire, or moss) each of which can be injured or lost. Each creature has a discrete mind and individual personality, including likes and dislikes, and possesses specific trainable or innate skills in various labors and abilities, as well as short and long term memories to facilitate all this, as well as influencing its current emotional state."
It influenced later games like Minecraft and Rimworld, and is still alive and kicking, with 2022 version adding actual graphics instead of text-based graphics.
