I've run tournaments in all three games, but I run each event separately. For the rulesets of each game, I pretty much used the standard Melee rules (established over a long time by the competitive community) and changed them slightly to accommodate the differences between the games. There are going to be some things that apply to all games (advanced slobs for counter-picks, no items, etc.) and some things that are specific to the game (amount of stock, time limit, stages, etc.).
Here's a few things I recommend:
-Brawl = 3 stock, 7-8 minute time limit
-Melee = 4 stock, 8 minute time limit
-64 = 5 stock
-use SBR rules for Brawl and Melee, and adjust the stage bans at your own discretion
-for 64, I'd suggest banning Mushroom Kingdom, Yoshi's Story, and Sector Z, and use Hyrule + Dreamland as starters
I hope that helps.