What is the location of the house? What are the insulation values for the exterior walls and attic? Are you going to heat and cool the walk out basement?

It is hard to imagine a 3700 sq. foot house needing 200K BTU of heating. That is very over sized. The 9 tons of cooling is absurd especially with a 5 ton unit for the first floor.

All of these quotes have problems. You need to find a contractor who will do a heating and cooling load calculation (Manual J) based on your plans. Once the sizes are established then you can begin to select equipment.

Southwestern PA
R-21 for exterior walls & R-38 attic, I think.
Yes, basement will be heated/cooled.

The third contractor (9 ton) told me he performed the calculations (twice).

There are approximately 50 windows in the home (including basement), if that matters at all. Andersen A-series high performance, low-e4, double hung (mostly). About 900-1000sq ft of windows.

You have above average insulation which makes the sizes even more wrong!

Ask the third contractor for a copy of his calculations. Review it yourself and see if it makes sense to you. The copy should state the version of software he used. If possible post the summary and you should get some comments.

Yes it does matter. Sizing requires exact numbers for your home and not approximations. To be honest, the oversized equipment being proposed for your house (based on the little you're telling us) is absolutely inappropriate and obnoxious.

Just realize that less is more when it comes to HVAC, especially if going with single-stage equipment. You will end up being less comfortable with oversized units, not more. :)

Are all 3 oversized?

I was talking especially about the last two options, it's almost bordering on the crazy. Although you can't get exact numbers without exact information. For instance, you haven't even stated your location,

Based on your limited information (and your way above average insulation) you could even get away with 2 2-ton units with WAY less heating. Like Mike said, have a Manual J performed, pay out of pocket if necessary. I personally wish all states would make it mandatory. A manual J will end up saving you way more money than your current proposals will ever provide.

Yes all three quotes are over sized. The first one is closest for AC. The second floor is probably in the 2.5 - 3 ton range. But then the first floor can't also be 3 tons if it has the similar area and windows. The 9 foot ceiling does not add much to the cooling load.

I would think the heating load of the whole house is less than 100K BTU. So one 100K BTU furnace would be sufficient. All the heating estimates are off by 100%.

There are free on line calculators to do your own calculation. Or you can buy a copy of software on line for one time use for $49.

It's not that hard with the software. Basically, you feed it the square footage of each room, the type of insulation in outside walls and size/type of windows. You tell it what temperatures you want for winter and summer and what the averages are for your region. It sits and thinks and spits out numbers, usually in BTUs for heating and cooling. From that you get your tonnage for cooling and BTUs for heating.

BTW: I might be asking for a bit more insulation in the attic if this is new construction. R-38 would be a little light for me. I might be looking for R-50 in Penn.