There is both long and short limb gastric bypass surgeries (along with several other variations on intestinal bypass procedures). How much of the jejunum is bypassed with a long-limb and short-limb gastric bypass?
One of the most used surgical technique is Roux en-Y where the small intestine is divided approximately 40-50 cm below the lower stomach outlet and is re-arranged into a Y-configuration.
The portion of intestine (jejunum) from the upper stomach is called the "Roux limb". It has a total length of 80 - 150 cm.
So the Roux en-Y technique "bypasses" only the duodenum and a small portion of jejunum - no more than 50 cm, that's about 7-10% of total length of small intestine.
Reference: Wikipedia contributors, "Gastric bypass surgery," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Gastric_bypass_surgery&oldid=606081291 (accessed June 27, 2014).