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Ethaniel made three really good points. First, and most important, is the basement rough-in. Also, the mechanical room. I've seen way too many crappy layouts for basements. All it takes is a few minutes of logical thinking, but alot of builders just don't do it. Look at it yourself.

Plus he mentioned a couple of exterior things that will come in really handy down the line. Exterior plugs, particularly in the soffit with a switch for xmas lights, and an extra hose bib. Another thing builders tend to do is put just one hose bib outside, so you're stuck running hoses all the way down the side of the house for either front or back watering. Check to make sure there's at least two.

Something else to consider is cable and power up on the wall in the master bedroom for a wall mounted TV. They're popular and cheap these days, and it's reasonable to assume that you'll have one or that future buyers will have one. If you're really on the ball, you'll request a bit of extra backing for added support where you mount the TV.

Avoid pocket doors entirely, if possible, but especially on the main floor of a two story home. They're a major bitch because the weight of the house eventually causes them to not work properly, and they're quite expensive to fix (tearing up the wall, re-drywalling, taping, painting).

Be careful with the his and hers sinks in the master ensuite. If there's not enough room for two people to do their thing simultaneously (don't wanna be bumping elbows), then there's no point. It'll take away from counter space and your wife will not be pleased if she has to put her hair dryer on the toilet because there's no room on the counter.

If you get a 5 piece ensuite, make sure there's a light in the shower.

You may want to have security system and central vac rough in.

French doors in the great room often destroy what could be a great furniture layout. I'd probably go for a regular man door. And if your garage is in the back, and you plan on parking in the garage, you may want to try to get the rear door oversized. Think about all the times you're going to come home with groceries or hockey equipment.
In case you do that, try to replace the french doors with an oversized window. They look great.

A skylight in the master ensuite is awesome. I have no idea what kind of spec you're going for, but if that's within the budget, it really does help sell the home. If not in the master ensuite, then above the stairs.

If you're getting hardwood floors, get flush mounted vent covers. They look way better than the plastic or metal ones that protrude from the floor, and they're not very expensive.

Again, depending on your spec, a couple more things to consider for the kitchen... Undermount lights on the cabinets and an automatic light in the pantry. You'll love the undermount lights at night. Just a perfect amount of light eminating from the kitchen. You leave them on all evening and don't really feel like you're wasting electricity.

Vaulted ceilings in the master bedroom is another big selling feature. Expensive, though.

Be sure that any built-ins have logical electrical and cable outlets. Nothing worse than an ugly cable running across a nice built-in because you wanted the TV on the other side.

If you get a jetted tub, make bloody sure that the builder puts in an access panel. Trust me.

If you decide to get granite, start with kitchen, then do powder room (main floor 2 piece washroom), and if you've got the cash, go for the ensuite last. Reason being, guests will be using the main floor powder room. And afterall, we're all trying to show off, right?