Jerkiness comes from all sorts of sources such as...
--A too-smart exposure algorithm in your camera that hunts the exposure around in response to the changing contrast of your scene. Best to be in manual exposure mode. Some (I'd say most) auto exposure cameras "quantize" exposure in leaps of 1/3 stop or so, rather than varying the exposure in small increments.
--Wind moving things around...if it's a windy day don't allow trees, plants, or anything windblown in your foreground.
--Exposure variations from clouds passing in front of the sun. This is a particular problem at slow frame rates, best to keep the frame rate up in these circumstances to record several frames of each light change, rather than having sudden, uneased changes. In post you can slow down the effective frame rate later by averaging frames together, say frames 1-2-3-4, frames 2-3-4-5, frames 3-4-5-6 etc. Smooths things out. Even high clouds you might not even notice can vary the exposure by a good fraction of a stop.
--Variations in the camera itself.
--And of course an uneven exposure rate.
There's a good argument for using Canon point & shoot cameras for timelapse. There's a freeware program that you can temporarily load into many Canon cameras via the flash card which allows sophisticated timelapse and other neat stuff. You need some geek DNA to make it work, but it's worth the effort...http://chdk.wikia.com/wiki/CHDK
Nice thing about the point & shoots is they are cheap (compared to a DSLR) so you can think about leaving them unattended in remote locations. And the there is no flapping shutter to wear out. I've heard of people who rig multiple cameras on clamps attached to tree branches and such, shooting several scenes at the same time.
EDIT...all of which reminds me that if you can do wholesale frame averaging out in the 2 or 3 second range, you can get some really magical results from motion in your scene. Jerky tree movement turns into a weird, slow undulations, traffic dissolves into rivers and the re-assembles at stop lights, etc. There's a good short film in there somewhere.