When looking at upgrades, your buyer's agent can help you tremendously in deciding where to put the money and get it back when the time comes to sell. (Again, YOUR buyer's agent, not the builder's representative or design consultant!)
Musts:
42" cabinets in kitchen
Double sink in master bath
At least the garden tub, if not the jets.
Upgrade standard tile
Fireplace
Maybes:
Flooring: A lot depends on how long you plan to be in the house, and how you'll use it. Personally, with two preschoolers and a cat with stomach issues, we weren't spending an extra penny on carpet - we'll replace it before we sell, regardless. Maybe sooner. However, make sure you don't have carpet in high traffic areas, such as a foyer or hallways on the main floor. Many builders extend the hardwoods in the models, but will price it as an upgrade to take it beyond the foyer.
Linoleum: Most people don't like it anywhere in any home over $250k. HOWEVER, the builders know that, and overprice the tile or hardwood upgrades. Get contractor estimates, it may be a better deal to have it done after closing.
Countertops: So much depends on price range when you want to know what future buyers expect. Usually, cultured marble in the bathrooms is fine, but you don't want formica in the kitchen if you're over about that $250k mark.
"Invisible" upgrades: HVAC, hot water heater, insulation, carpet padding, running a gas line for the range or the dryer... These are upgrades that will pay for themselves in energy savings and use in the long run, but because they're not "pretty", most people forget about them. Some of these, the builder will require be paid upfront, possibly non-refundable, because they don't get that back if you bail. Again, your buyer's agent can advise you on these.
Other things like granite vs. corian, wrought iron vs. wood spindles, and decorative tile work are, imo, personal preference. If you plan to stay in the home more than 5-7 years, keep in mind that decorating styles usually go on about a 10 year cycle, so what is stylish now will need updating in 10 years - even that awesome granite, especially if you use a bold color palette. Not everyone agrees with me on this, but before you spend $50k on your kitchen alone, consider the above timeless items first, then with what you have left over, let your inner decorater free.
Things like extending the deck, putting in a screened porch, landscaping... all of that can be done after closing. Go ahead and get estimates from outside contractors if you plan to have those things done.
And no wallpaper.
