Happens to me too and I cant ignore it.. grr
I have an 04 6mt. whenever I let my foot of the gas pedal at around 2800-3400 it jerks a bit. Not too hard but its noticable.. It does it in 1st 2nd 3rd and 4th. Does anyone know a fix for this? I went to the dealer and I was told its normal..

 

Time to invest in an engine torque damper.

 

Its not the engine causing this, its the small amount of slack in the driveshaft. The driveshaft has to have some slack in it for the durability of hard shifts. If it was 100% tight, hard shifts would be terribly harsh on the driveline and transmission. This may be more pronounced on some cars, but as was stated previously, all MT's have this characteristic. The easiest way to overcome this as best as possible, is to always have ur foot slightly on the throttle, and if your rolling around at very low speeds, stay OUT of 1st gear.

 

i think the flywheel has an effect on this.

if you leave an automatic transmission in 1st or 2nd gear, you will have the same sensation.

 

I believe this as well, but in an auto, it is MUCH less pronounced. The heavier the flywheel , the lesser the characteristic. In my momma dukes' Chrysler 300, it is virtually non-existant, but the flywheel on those cars are extremely heavy. If I rev it to 5K rpm, it takes a good 5 seconds or more for the revs to fall back down to idle