I think there's a huge difference in the impact of an online or email petition and a letter or a phone call. There's no way to verify that all those online signatures are, in fact, real people or constituents. So the opinion of the signers isn't much use except as a publicity ploy. (Which has it's own benefits.)

One of my Reps informed me (at a breakfast meet-the-people meeting he has occassionally) that electronic petitions are pretty much ignored. On the other hand, letters and phone calls are carefully. Volumes of worthy (or unworthy) prose are only read enough for the clerk to figure out what it is you're talking about and whether you are for or against it. A short, concise note will suffice.

Email handling is a mixed bag. Some Congressman treat it like a letter, some don't. I happen to know mine DO tabulate emails if you use their web site forms (that check your address against their constituancy), but if in doubt, send a postal letter, or a fax, or call. Some Congressman are behind the technology curve. :)

Speaking of meeting your reps, a lot of them do have occassional meet-the-public events, where you can really have your say if you are polite and brief.