It could be the throwout bearing gone bad or perhaps some damage to the clutch disk or pressure plate causing it to be out of balance. Does it smooth out when you push in the pedal? Either way it sounds like a new clutch is in need. It should cost about $400 to $500 for parts and labor. At least you won't have to do it again for a long time! How many miles are on it? I have a 98 as well with 121k miles on it. I think it's still got the factory clutch in it. It seems it should take hold a little sooner than it does, but it's smooth and strong still. Much luck on it!
The crazy1 is correct but I doubt its the disk or pressure plate. Most likley (not in any order) pilot bearing, throwout bearing, improperly machined flywheel, or check the cable to see if its an adjustable one make sure its not out of adjustment.
Do you mean that the pedal vibrates from mechanical engagement, or that it vibrates like "change in a cup holder"?
My clutch pedal vibrates sometimes because I have vibration issues in my chassis. It is similar to jiggling the pedal lightly with your hand. If that is the case, I wouldn't worry too much.
Now, if your clutch pedal is pulsating from the motor/tranny running, have it checked out.