I am building a new home. I would run the wires myself, but I'm not allowed. Below are some are the quotes for 3 different options. The conduit or the bundled cable seem me to be the best deal. I also have the option of running speaker cable for $75 per drop. Any advise is appreciated. Thanks!
I'd say put in conduit - and go bigger than 3/4" if you can. Then you can go back once it's built and pull Cat5 yourself. Then, if you ever need another Cat5, you can add it. If you ever want to put in Coax, Fiber, or other low-voltage cable, you can. The cable is cheap when you buy 1,000 ft spools - I think I purchased 1,000 ft. of riser-grade Cat5 from Lowes several years ago for $50 - still have at least 250 feet of it too.
I highly recommend having conduit put in if you're planning on staying in the house for a long time. I ran my own low voltage wiring (2 Cat5e, 2 RG6) when my house was built a couple years ago, and now I'm having a difficult time adding new wires because I did not put in any conduit for growth options. I'm wishing now I ran more Cat5e/Cat6 instead of RG-6
For the structured wiring box, make sure there are multiple large conduits run from the box into the attic space as you will want as much room here as possible to pass wires.
If you have room, you may want to consider more than one structured wiring box for future growth. I outgrew my structured wiring box and ended up moving most of my equipment to a rack.
I made an assumption that the conduit would just be run to the attic space, which may or may not be true. You might want to get clarification on how the conduit is actually run.
If the conduit is run from each room to your structured media box (which is ideal), then you might want a spare conduit running into an accessible crawl or attic space in case you want to run some wires from a location that did not have a conduit run in the first place.
EDIT: Since you'll most likely be adding the wires after insulation/drywall/etc, it's critical to understand how the conduit will be accessed. Just because it's there, doesn't mean it will be easy to get to!
How big is big enough for conduit? Is running conduit to the attic a reasonable replacement for running conduit to the rooms on the 2nd floor?
The largest you can to the attic from your central location. Presumably you can access most of where you might want to pull wire on the 2nd floor from above in the attic, so as long as you have conduit in place to there then you should be okay. If you have spots on exterior walls they can be difficult to get to, so you might want to consider running conduit from those locations on the 2nd floor to the attic, depending on whether you can access that later based on your roof construction...
I would also have them do the basic structured wiring of 2cats and 2 rg6.
Don't know if it's possible but do you have the option of running the bundled wiring AND conduit? If so, I would have the bundled wire run to each room (option #3) and then have conduit run to specific locations (assuming they will let you decide where the conduit is run). I don't know what you may want in the future, but some places you may want to run conduit include future distributed audio keypads, locations of any touchscreens, and/or places where you may want a TV in the future (ie: the kitchen).
Also, DEFINITELY plan to have the speaker wire installed in the TV room for a 5, 7, or 9/10/etc speaker setup! You may want to have speaker wire run to the kitchen and another room or two for future audio distribution. Depending on the accessibility you have to run future wires, $75 per speaker wire drop is worth it!