I am creating logos or illustrations which display as pixelated lines. I am using the pen tool, any settings i should change or any tool i should add?
I assume you're talking about the pixelation...
You have pixel preview enabled, which shows your work as it would look rasterized at 72 PPI. Disable it from the View menu (View → Pixel Preview) or cmd+alt+Y.
As for JPG; that is a raster format (i.e. made of pixels) so you will obviously see the same. To keep your lines infiinitely crisp, you need to save to a vector format.