Obviously, you could do the Shiny Ditto trick to get every shiny in Gold/Silver/Crystal, but if you havnt got the coloured games, then this might work.
Ive just worked this out, so sorry if there is any mistakes.
Try this to get as many shinies as possible:
1. Catch a MALE Red Gyarados at the Lake of Rage.
2. Breed this with FEMALE versions of every Pokémon in Gyarados' groups:
Group 10 - Water Dwellers (C)
Group 13 - Dragons
3. Make sure each offspring is shiny, and the ones mentioned below are MALE (yes, alot of soft resetting).
4. Breed selected MALE offspring (below) with FEMALE versions in their corresponding groups:
Group 7 - Forest, Wood, Ground Dwellers - must use Ekans
Group 8 - Water Dwellers (A) - use Horsea, Dratini or Remoraid
Group 11 - Beasts - must use Charmander
5. Again, make sure each offspring is shiny, and the ones below are MALE.
6. Breed some MALE offspring (below) with FEMALE versions in their other groups again:
Group 1 - Shrubs, Plants, Weeds - use Bulbasaur or Chikorita
Group 9 - Water Dwellers (B) - use Omanyte, Kabuto or Corsola
Group 12 - Magical - use Pikachu (evolve Pichu), Marill or Snubbull
7. Yet again, make sure each offspring is shiny, and Paras is MALE.
8. Breed the Paras MALE offspring with FEMALE versions, again in its other groups:
Group 2 - Beetles & Bugs - must use Paras
As far as I know, only the above groups are breedable this way. Make sure each offspring is shiny, remember.
These groups are missing:
Group 3 - Birds & Bats
Group 4 - Humanlike
Group 5 - Rocks & Minerals
Group 6 - Supernatural & Pollution
Group 14 - Mysterious
And the ones that dont breed, obviously.
Youll have to catch these lot yourself. Unlucky, but remember, try to breed MALE shinies. It makes it easier to breed new shinies.