This might not be what you're looking for, but I use an Excel spreadsheet that autocalculates NPCs and critters. The way it's set up, you can create three NPC cards per page: I print em' and cut them out to use as initiative cards: i.e. track my bad guys stats/HPs/etc. and the initiative of the battle in one stack of cards (I have the PCs use blanks sheets since I don't need their stats in combat usually). Anyway, it's still a work in progress, but you might find it useful!
Here were the types of problems I encountered. Maximize spell feat only being able to be used on ray of frost (for a 16th level sorcerer). Magic items always being weapons and some potions, never a scroll or wand. With a little tweaking these were fixed (weapon changed to rings of protection, some spell swapping to put in lightning bolt, etc.) but the warriors were significantly better "out of the box" with appropriate feat chains connected to weapons, etc.