I thought this might help people starting out. My architectural designer wasn't very good with detailed work at all, and when everyone says 'specify EVERYTHING', they really mean it!

Interior elevations - we're first time builders, and didn't realize that plans could be passed through the city without interior elevations!

Shingles (craftsman style house) should be stained, not painted.

Exact size of exterior trim as well as material. (Azek seems to be the consensus here) Also make sure the fascia is Azek, otherwise you get wood, which will have to be repainted every so often.

Exact size and type of interior trim. They spec'ed out 5+" baseboard and single stack crown moulding, but I guess that's standard baseboard, and I now think bigger would be better for craftsman style. I would have gotten a pre-contract bid for wood trim vs white trim.

Front entry steps were not spec'ed, so they bid it as wood. I now realize we really want concrete, or something more substantial than wood steps (like a back porch!).

Fireplace gas insert and mantle - it's included in my bid, but now I realize that it's not specified as to what type, and also, the average mantle is shallow, maybe 7-8". You might want something deeper for your holiday decorations.

Surround sound wiring in the family room, basic wiring for tv to your receiver closet, and in-ceiling speaker wires. At least get a specified bid prior to signing, so you can know what you're dealing with.

I AM happy that I specifically asked re: Tyvek, upcharge for wood interior doors vs solid core, windows (one brand vs another), roofing materials, heated floors for the bathrooms, smooth finish for drywall (more expensive than the knock-down finish) gas and water lines exteriorly to the big porch, concrete retaining walls for the back yard (well, they're there with the concrete truck anyway...it HAS to be cheaper than having landscaper do it later!). Also happy that we had discussed phone/cat-5/cable wiring to be run inside smurf-tubing/conduit(thanks to members here!). Glad I sat down with the arch. designer and did the electrical/lighting plan, since he would have completely underplanned it! I do wish that I'd put in-cabinet lights into the plans. We have a list of 'allowances', and just one big number for that, and it works well. It allows me to shop for my fixures and flooring and cabs at discount places as well as on craigslist. The plumber has no problems with it.

I guess it comes down to whether you trust your builder to NOT look at changes as a financial opportunity, and I'm very happy that I had specifically discussed that with them before. They've been reasonable so far, as far as I can tell, but it's definitely the case that there's much more negotiating power BEFORE the contract is signed, and if you decide to upgrade to the surround sound, at least you know they won't charge you double for it later, since you have a quote for it already. My coworker got a $10,000 change order for changing his living room entryway from a rectangle to an arch! I suppose I'm happy that my guy only charged me $1000 to move a window up 10" (after installation, but prior to insulation/drywall).