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We use our gas fireplace a lot too, especially the one downstairs. And it could hurt resale value as well.

Cat5e everywhere is a great idea. Wireless is nice, but can be flaky in a big house depending on what's where; having a cable means you'll never have to worry about it.

Another related one is to get a conduit run from the attic down to wherever all the cabling comes together; lets you install things on the roof without having to have wires run down the outside of your house. I've spoken with guys that have gone in and run conduit around their house just for cabling down the road.

Granite and as much tile and hardwood as possible; we even have hardwood in our bedroom. So much easier to keep the floors clean (I hate carpet) and for the counters so much more durable and easier to keep clean as well.

High efficiency furnace(s); I really regret not doing this.. or at least a multi-stage furnace so it can run quietly.

We flipped the back half of our house so we could have a walkthrough pantry from the garage through to the kitchen; great for bringing in groceries.

Bigger baseboards and smooth door faces are upgrades that are pretty cheap but can really make a big difference in the look.

Agree with Shazam, wider garage!

Another inexpensive upgrade (depending on the cabinet maker) is higher cabinets, and then extending the cabinets to the ceiling. Ours are very tall, then at the top there's a crown molding (or whatever it's called), and then another piece of wood that goes all the way up to the ceiling with another piece of trim up there. Removes the dust gathering up there and makes a big difference in the look.. and for us it was pretty cheap to do too, but I've heard other cabinet companies charge a huge amount for it.

We also did a drop down ceiling above our kitchen island and painted it an offset colour; again a fairly cheap thing to do but makes things stand out more.

Do something with the outside train spouts so you don't have one over your main entrance sidewalk (if applicable).