These three Legendary Pokémon have no specific location of where you can find them because they are always on the move throughout the Gold and Silver map. Once you run into one of them you can always keep tabs on where they are by going to your Pokédex and then checking their location (the first choice at the bottom of their entry).
But first, if you haven't already waken them up you will have to go to Enjiu City. Go in the Tower pictured, break the rock in the way and fall down the little hole. Walk up the stairs and they will awaken and scatter.
Lugia(silver)
Lugia is a little harder to get. You'll need a Pokémon with Surf, one with Whirlpool, and one with Flash to get to Lugia.
Go to Asagi City and surf south trying to stay as far to the right as you can. There is 4 entrances to the cave where Lugia is so if you follow the wall the first one you come to is the one you need to enter.
Once inside go to the right and choose the top path when it comes to a fork. Now you'll make your way to a waterfall, go down it, then surf up and you should find Lugia swimming in the water.
Lugia is also level 40 and will give you 1257 experience points if you beat him. But DON'T, what are you crazy or something!? Again, using the Master Ball at this time isn't wise.
If you wanted to know, Lugia learns Hydro Pump at level 44.
Lugia(Gold)
Yes,
Lugia can be obtained in the Gold Version, you just won't be able to
get it as soon as you got Houou. In Pewter City there is a man who
will give you a Silver Feather. Take this Silver Feather and head to
the same place as Lugia is in Silver and you will fight a level 70
Lugia.
Houou(Gold)
Houou is really easy to find compared to Lugia. Go back to Enjyu City and go into the northern house. Go in all the stairs and you'll eventually come to a tower. Go inside, work your way through the maze inside, and once you make it to the roof you'll find Houou.
You better save your game before fighting Houou, because like Mewtwo, there is only one. Houou is only level 40 so using the Master Ball isn't a good idea.
Houou(Silver)
Yes, Houou can be obtained in the Silver Version, you just won't be able to get it as soon as you got Lugia. In Pewter City there is a man who will give you a Gold Feather. Take this Gold Feather and head to the same place as Houou is in Gold and you will fight a level 70 Houou.
Special Colored Pokémon
You remember the Gold Gyarados in the lake north of Choju Town right? Well that's not the only Pokémon that is colored differently. Throughout the game, through all wild grass, there is always a very very very slight chance you'll run into one of the special Pokémon. They have beefed up stats and are a lot better than the normal "regular" colored one.
To make sure you have a special colored Pokémon look at its stats and if it has 3 pluses by it's gender, then that means it's a beefed up one. Also, when used in battle it will sparkle and shine
when you bring it out.
Baruki
Baruki is pretty well hidden in the mountain in between Enju City and Choju City. Hopefully you'll be able to find him with these pictures. And remember, you must only bring 5 Pokémon with you or you won't be able to take Baruki with you. What you will need is a Pokémon with Flash, Surf, Waterfall, and Strength. Baruki will evolve into Hitmonlee at level 19.
Surf passed the first mountain entrance east of Enju City and enter this middle one. Surf into the water right at the entrance and head north up a waterfall. Head through the door and you'll want to keep to the right on the other side. You'll need to surf across water and navigate through a semi-tricky maze to get near the top. You'll find this ladder leading down at the top left corner of the maze. This portion of the maze is pretty simple, when you enter head to the right and up and around until you get to this ladder. Defeat this Karate guy and he'll give you Baruki.
Marill
And don't forget to get Marril on your way out of this cave.
Lapras
Lapras is another fun Pokémon to find. In between Kickyou City and Hiwanda Town there is a cave that you can navigate through to find a lone Lapras swimming by itself.
Lapras can only be found on certain days, so far Friday and Saturday have been confirmed.
Yadokingo
Yadoking evolves from Slowpoke, you need to have ''symbol of king'' equipped on Slowpoke. Symbol of King is found in the cave where you freed the slowpokes from team rocket, there's a person down there that will give it to you. You need to have surf and strength.
Eevee
Stop by this house in Kogane City to get your own complimentary Eevee. Have a slot open for it though or you won't be able to get it.
Another way to get Eevee is by going to Celadon City and paying 6,666 coins for one in the Game Corner.
To get the Psychic Eevee, Eefi, level up Eevee during the day.
To get "Blackie", level up Eevee during the night.
Aerodactyl
Here's a trade you can find on Route 14 which is East of Vermilion City. This girl is looking to trade her Aerodactyl for a Chansey.
Chansey can be found in the same grassy area where the girl is standing but good luck running into one because they are very Scarce.