I don't sweat NPC skill points. If I need them I'll assign them on the spot.
I use
d20srd.org for a lot of referencing.
I have a lot of pdfs, printing off just the page for the monster I plan to use keeps it a lot more manageable at the table, particularly if I plan to use monsters from different sourcebooks. Plus you can highlight things like DR on a printout without ruining your books.
"All right then, your delaying. Let me know when you decide and you can jump in then. Next."
"That's my ruling, we're not debating or discussing it anymore right now. We can talk about it after the combat/game."
Keep in mind that keeping the game moving and fun can be more important than getting every rule exactly right by the book.
I like using modules.
I try to avoid using things I consider less fun or house ruling them. Ability drains generally turn into ability damage, save or die I house ruled to save or dying, I dislike having PCs regularly incapacitated for a whole fight so I like the 3.5 hold person save each round to shake it off and want to extend it to other effects.
Use resources like the NPC wiki for stats instead of creating from scratch.
PC equipment out of whack? Rust monsters, Druids with warp wood and rusting grasp, tons of monsters with improved sunder.
I go with spontaneous divine caster option from Unearthed arcana (clerics and druids cast and know like sorcerers) so that I don't have to consider impacts of every divine spell for visimilitude, just the ones I want to be there. (I.E. why don't we ask the local priest to do X).