Get Lugia on Soul Silver without Cheating

Catching Lugia on SoulSilver isn't that hard, even without cheating!

Steps

Get everything you need. You must have already received the Silver Bell from the Kimono girls in Ecruteak City. You also need the Silver Wing, and Pokémon that know Surf, Whirlpool, Waterfall, Rock Smash (optional), and Strength. Whirlpool islands are unlit, so having Flash as well is worthwhile. Having Pokémon with status affecting moves is also very helpful. (i.e. Sleep, Paralysis, Frozen, etc.) Remember to also have plenty of Ultra Balls.
Go to Cianwood City.
Then, go to the Pokémon Center and make sure your Pokémon are level 40 or so. A strong Electric- or Ice-type Pokémon helps.
Make sure you have plenty of Repels, unless you want to run into a lot of Pokémon on your way there.
Use Surf and try to find the Whirl Islands. It should be the one with two swimmers near the whirlpool blocking it. You should be entering the island part from below.
Now this is the tricky part. It's pretty much your average Pokémon cave - a maze.
The right place will be blocked by an old man. He will let you through if you have the Silver Wing.
Go down and into the cave with a massive waterfall within.
The Kimono girls should come in and talk to you before preforming a dance to summon Lugia.
Once it is over, Lugia will appear! Surf to it and press A to begin the battle!
Play your cards right and you'll have Lugia!

Lugia is also available in HeartGold, but it is level 70 and you have to get to Pewter City first instead.
Stock up on Ultra Balls, have an Escape Rope ready so you can leave without going through the labyrinth again, and heal your party before going in.
Keep lots of potions and some PP Up if you can.
If you have received a Master Ball, DO NOT use it on Lugia. Save it for Mewtwo in Cerulean Cave.