Some vibrating I can't shake?

[Zombiesrock]

So, I am new to this forum, even though I have had my 07 yaris hatchback since Dec of 2006:)
I love my car dearly, even with its issues. Lately, for months now actually, I have noticed that when I am in gear at a stop my car vibrates excessively. It doesn't in park or in neutral. When I say excessive I mean you can see the engine shake quite violently. looking at the engine move my husband thought it could be rear motor mount. The engine torque mount? Any way we took it out and checked it and it was fine, so my husband watched my cars engine through all the gears and thought maybe it could have something to do with my automatic transmission clutch not fully engaging. Also when I was trying to diagnose the problem by reading other posts, I found it could maybe be the brake booster. I am not hearing any whistling etc, and its not a gentle idle. Also my clear coat seems to be bubbling and peeling off on major parts of my car.
I have 140,000 miles on it. I have washed it every month and waxed it (including clay barring etc) every 5 months or so. we change the oil every 3k (granted sometimes i do go over that) and never have any other problems. Hell, I hit a deer doing 55mph full on when I only had 26k on it, had it fixed and still never any issues. (the deer caused $7k worth of damage)
So any help on these issues would be great.
Thank you all for loving your Yaris' enough to have a forum like this. It really has been very helpful.! Oh and I have no check engine lights and am not sure if it could be a misfire. the third sparkplug from the left had a little more white fuzzy stuff on it than the other three, but they appeared to be healthy as well.

[CTScott]

The vibration when stopped complaint is a very common one. When I acquired my deer hit 08, it had a very noticeable vibration when stopped in comparison to my 09 (both being automatics). I found that using the ebrake instead of the brake eliminated it as did fiddling with how much I pressed on the brake pedal. I swapped out the brake booster and it went away completely. There was no audible indication of the booster leaking, but apparently it was leaking when the pedal was fully pressed.

The RPMs do drop when stopped without a load (AC on, etc). If the engine is running perfectly, this drop in RPM will be far more noticeable (as vibration). So, vacuum leaks, dirty injectors, fowled plugs, dirty MAF sensor, carbon deposits in the throttle body, weak coil packs, etc. can all be potential causes.

[Zombiesrock]

Whew! That sounds a lot to check. Thank you for responding though, I will just make a list and start from the beginning.