The intake manifold is extremely important, as it's the door for the air/fuel mixture to enter the cylinder heads. You'll see various designs of intakes, mostly centering around "dual-plane" and "single-plane" intake designs. A dual plane intake has a divider in the plenum (under the carb or throttle body) that provides two plenum areas for the engine to draw from. A single plane's plenum is open--just one common area for all of the runners to draw from.
Generally speaking, single-plane intakes are suited more for higher-rpm engines or race applications. Most offer very large plenum volumes and short runners that can be easily ported and shaped to flow more air. The only issue with large runner volumes is that it tends to give the same effect as a cylinder head with large port volumes. It takes momentum to get the mixture moving and sometimes it requires more rpm to get that momentum. Dual-plane intakes are suited more for street applications, as they tend to offer more power in the lower/mid range powerbands due to their longer runner lengths. You'll also often see a better equalization of the fuel mixture to the cylinders, as the intake is divided instead of every cylinder having to pull from a large, shared, open plenum. This is more of a concern in carbureted applications where the fuel is not injected individually into each intake runner.
In the same fashion, a large engine can “dumb down” an intake manifold. Larger engines need much more volume so that they can be fed effectively. For instance, an Edelbrock Victor Jr. intake on a 302 can offer sluggish street manners, but it would be a perfect choice for a Windsor in the 427- to 445ci size.
Carburetor spacers can be used to modify the intake manifold's plenum design. Adding an inch or two of space between the carb and the intake can allow the fuel mixture to pick up some extra velocity as it enters the cylinder head. It can also add plenum volume to an intake manifold that may be a little undersized in that area. There are open spacers, four-hole spacers, and combination spacers. It's hard to put an exact description of what each spacer would do in a certain situation, but very generally speaking, an open spacer will add horsepower while a four-hole spacer will add torque. However, engines don't always understand this rule of thumb, and you can often be surprised at the result of adding each spacer, tapering a spacer, turning a spacer upside down, and so on.
What's our motto? Yep, build the engine for the application. As long as you keep that in the front of your mind, you will do an excellent job in the design of your new engine. If you're more adventurous, you will learn a great deal if you hand-pick each component. Choosing the cylinder heads to match the engine's desired manners, picking an off-the-shelf cam (or even ordering a custom cam made to your specs) to make your engine perform the way you want, and then topping the engine off with the correct intake manifold will give you a great feeling of accomplishment and increased knowledge.
If you're not one of the adventurous types and you'd rather use a company that puts together its own cylinder head/cam/intake packages, then there's absolutely nothing wrong with that. You can still decide what the desired result will be, then carefully look at the packages that are available from manufacturers such as Edelbrock, Trickflow, AFR, and so on to obtain that desired result. Plus, there's no rule that says that you have to keep those same components; you can always do a cam swap, intake swap, and more, to see how different items will make your engine behave.
The bottom line, however, is that if you start off with a good foundation (your engine block), good machine work, and select the parts that make the engine fit the application, then you will not be disappointed.