-Take Immaterial's stolen-from-Wrex houserules. The whole thing.
Don't do this. It was specifically designed for high-powered games, ie the kinds of games that need an experienced DM to run. Also, you won't likely understand
why a lot of the changes were made, and that's a recipe for bad things.
Not to mention that there have been changes made to it by several people other than Wrex, in at least a couple of cases for "realism" by people who don't actually get what the rules were intending to simulate, or, indeed, the mechanical effects.
-If you write your own pantheon, for the love of said gods make it good. Cover every alignment. Make doubles for the neutral ones. Make the righteous dick god for paladins, and make the stoner hippy god for druids. Make your best gods patron deities of something--races, classes, ability scores. Include a pair of opposed gods. Make the Grim Reaper ripoff and the Judeo-Christian stand-in.
Don't feel tied to this. The first half is generally valid advice, but chaining your setting to existing stereotypes is not necessary. Remember, Clerics outside Forgotten Realms do not
have to worship a given diety; a world with no gods, were Divine Magic is all drawn from concepts, or with just a couple of Gods who deal with a few particularly important things is totally valid.
-Most Bay12ers who play these are experienced. Take advice, especially if the advice-giver has run a game or two.
Most Bay12ers who play D&D here have little to no experience playing D&D anywhere other than Bay12, and games here are generally not particularly successful, for a number of reasons. I would suggest hopping on Bay12lb IRC and taking advice from a few of the people there; mostly Wrex, who is actually professionally involved in RPGs.
-Don't buff wizards and sorcerers beyond unlimited cantrips; same for druids and clerics. If somebody wants to be a monk or a fighter, redirect them to the Tome of Battle.
Expanding on this, be very cautious about buffing anyone at all, since you likely don't have the system mastery to understand what a seemingly-minor change can do to the game as a whole; D&D (particularly 3.5) is a very mechanics-heavy game, with a lot of extremely interlinked systems, and "fixing" one thing somewhere (often to make something more "realistic") can often horribly break a whole bunch of other things. Also, I wouldn't suggest unlimited cantrips.
-Don't include that character you wanted to play as a prominent tagalong NPC. It's the players' game, and with that character it'll feel like an escort quest.
Maximum agreement, for a whole bunch of reasons. That said, don't be afraid to add an NPC in to cover a character position that the group needs for the game but no-one wants to fill; a friendly Wizard (or even just a patron sending the group on errands) for a planehopping game where none of the PCs can actually hop planes, for instance.
-Don't be afraid to tell That Guy to shut the hell up.
Technically valid, but do also compare this to Tawa's advice to take advice, and remember that advice you don't like may still be valid, and a first time DM may not be the best judge of who is being That Guy, particularly if you fall into the trap of DMPCs, railroading, and otherwise trying to tell a story. Remember, you're playing a game, with other people, not getting actors to act out your book for you.