FF7 has a load of secrets and the only way to find them all is through Faqs and help guides. Here I will post the best of each type to help you through FF7, or help you find things you missed before. Let me just tell you to have patience with some of these things, doing things like killing Ruby, or Emerald or getting a Gold chocobo can be frustrating, but keep on trying and what you get will be well worth it.

Acknowledgement to the authors is listed inside the faqs, none of them have been written by me.

Final Fantasy 7 Walkthrough and Basic Info.
FF7 Extra Info and Lists.
The Chocobo Manifesto, Breeding and Raising Guide.
Monster Item Guide, things you get from stealing/killing monsters.
Game Shark and PAL Codes.
Guide to defeat Weapons. Guide to Date Yuffie (!). 1