Hidden Doors in Heart Gold and Soul Silver.
Ruins of Alph:
In Pokémon HeartGold and Soul Silver Versions, patterns appear on the walls of the puzzle chambers. When the patterns' directions are followed, doorways to hidden rooms appear, where the player can get many items and learn some of the history of the Unown.
First Chamber:
In the northernmost chamber, the far wall reads "escape" upon inspection. Using an Escape Rope there opens a hidden room upon re-entering.
In Heart Gold and Soul Silver, it does not consume the rope and instead the player gets an ! over their head, and the room opens.
Falling through to the floor below reveals the following message spelled out on the ground in Unown:
>"Our clan engraved words in this place".
In Heart Gold/Soul Silver, this chamber contains a touchscreen puzzle that forms Kabuto. Once completed, the A, B, C, D, E, F, G, H, I, and J forms of Unown are unlocked in the main chamber.
Second Chamber:
In the south-easternmost chamber, the far wall reads "light".
Getting a Pokémon to use the field move Flash will open the hidden room.
The floor below reveals the message:
>"Our clan created Pokémon statue outside".
In Heart Gold/Soul Silver, this chamber contains a touchscreen puzzle that forms Aerodactyl. Once completed, the R, S, T, U, and V forms of Unown are unlocked in the main chamber.
Third Chamber:
The third chamber is accessed through Union Cave but requires a boulder to be moved. The far wall reads "water".
The hidden room will open if the player has a Water Stone in their inventory, though, in Heart Gold and Soul Silver Versions, the player is required to select "Use" from the items menu while facing the wall for the room to open.
The floor below reads:
>"They possess power to sense with mind and reject outside".
In Heart Gold/Soul Silver, this chamber contains a touchscreen puzzle that forms Omanyte. Once completed, the K, L, M, N, O, P, and Q forms of Unown are unlocked in the main chamber.
Fourth Chamber:
The final chamber is also accessed through Union Cave. The far wall reads "Ho Oh".
If Ho-Oh is the first Pokémon in the player's party in Generation II, or anywhere in the player's party in Generation IV games, the hidden room opens.
The floor below reads:
>"We humans need to walk with them. We leave here for the sake of them".
In Heart Gold/Soul Silver, this chamber contains a touchscreen puzzle that forms Ho-Oh. Once completed, the W, X, Y, and Z forms of Unown are unlocked in the main chamber.
Items available in the Hidden Chambers in the Ruins of Alph:
First Chamber: Heal Powder 
, Energy Powder 
, Oran Berry 
, Pecha Berry 
Second Chamber: Heal Powder , Energy Root 
, Moon Stone 
, Sitrus Berry 
Third Chamber: Stardust 
, Star Piece 
, Mystic Water 
, Leppa Berry 
Fourth Chamber: Revival Herb 
, Charcoal 
, Life Orb 
, Leppa Berry
Team Rocket HQ
Although accessing Team Rocket's HQ is part of the storyline in the game, the entrance is still technically concealed behind a golden cabinet and thus is a hidden location.
To access Team Rocket's HQ you have to first either capture or defeat the Red Gyarados at the Lake of Rage. Once you have done that you have to go and talk to Lance, he will tell you that the Red Gyarados wasn't acting right and that it was forced to evolve. He will then ask you to help him out with his investigation and that a strange radio broadcast is being transmitted from Mahagony Town and this may be the cause of Gyarados being forced to evolve. He will then tell you that he will be waiting in the Souvenir Shop in Mahagony Town for you to arrive before flying away on his Dragonite.
When you get to Mahagony Town and enter the Souvenir Shop he will command his Dragonite to use Hyper Beam towards a random individual. He will then confirm that the strange radio broadcast is being transmitted from this location and walk up to the golden cabinet in the room moving it revelling the entrance to the Team Rocket HQ.
Inside Team Rocket's HQ you can find the following items:
Guard Spec. 
, Hyper Potion 
, Nugget 
, Revive 
, Full Heal (x2) 
, X Sp. Def 
, TM46 Thief 
, TM49 Snatch , X Special 
, Protean 
, Ultra Ball 
, HM05 Whirlpool 
