Since there have been several posters lately who have some past experience in how to contact elected representatives, I thought I'd add the perspective of a career federal employee to the topic.
I work for the U.S. Department of Commerce as an engineer. In that capacity, I work on projects that, for the most part, aren't of terribly high interest to most people outside the government. There are a few notable exceptions, though, that do attract public attention.
More on the other side.
So how do people get through to us, and let their feelings be known? Well, of course the most obvious is direct contact, either through emails, telephone calls or faxes. The information for contacting our office is available on the web; this is true for many (if not most) federal agencies and organizations. But the federal government is a pretty big place, and it helps to have a general idea of whom you're trying to contact.
My first bit of advice, then, is to do a little preliminary research to find out which office to call -- it will just make things easier for you. It's not that we don't like to get calls or emails (quite the opposite); rather, if you're looking for information that another office or department would have we will quite possibly have no idea who you should be talking to.
Another way that is effective is the use of on-line commenting systems that a few agencies have set up. If such a system exists, use it -- we DO read the comments.
The moral of the story is that attempts to contact the government do get noticed, and people shouldn't be afraid to do so. At the same time, a pretty good way to be ignored is to come off like a kook. Sound elitist? I'm sure it does. And we do our best to not ignore opinions that are simply expressed badly. But we're human, too, and believe me, we see all sorts of things. Comments and communications that are nasty, rambling, one of a thousand identical "form letters" or just plain "out there" probably won't make a big impact.
It really helps if you have your stuff together before you try to contact, too. Clear and concise writing or telephone calls can make a big difference.
It's wise to keep in mind that most government employees are not political appointees. While just about everyone has political opinions (government employees, too), in general government employees are there to do a specific job that may or may not have much to do with the policies of any current elected officials. The "government" is not a monolithic entity.
I'm sure there's stuff I've left out; if that's true, please feel free to ask.