Story Archer...I'm not normally a fan of houserules, though it never hurts to look just in case someone's come up with something brilliant.
Well, I'm making some character-specific changes to help them realize their concepts more fully, but those are unique things, not what I'd term official 'house rules'.
The main things I'm going to be doing is getting rid of Spell Resistance; for monsters who normally have it, 'Spell Resistance' becomes a monster ability which grants a universal +4 to saves vs. spells and spell-like abilities. I just find it really streamlines play.
I'm also adding BAB to Initiative rolls, something I've done in the past that has worked really well. Apart from that I generally ignore WBL and customize the majority of my magic items.
We had our official 'pre-game' meeting last night, finalizing characters and ironing out all the little things including character background. I've got one of the more 'techie' guys working on Roll20 right now to get familiar with it and I've even ordered the Deluxe Edition as a present to myself for being such an awesome GM ;-P
I'll keep you guys updated. I'm going to have them each keep campaign journals, and will be engaging them in RP via email between sessions to further the story and their individual subplots. I'm seriously considering making a website to tell the story as it unfolds, but I'm not sure there's enough interest in yet another RotRL campaign journal, even one as unique as this one will be.