Using ISI's Web of Science "Cited Reference Search", I searched for the term encyclopedia* to find the papers that had an encyclopedia mentioned in their bibliographies.
There are three indexes within Web of Science. The index that is the smallest - that being, covers the fewest number of journals is the "Arts & Humanities Citation Index". The index covers 1149 journals and for the period of 1996 to 2006, there are only 48
The "Social Sciences Citation Index" covers 1917 journals and from 1996 to 2006, there are 123
Not surprisingly, the Science Citation Index (Expanded) is the largest index within Web of Science. It covers 6543 journals and from 1996 to 2006, 114
Now one could make the argument that I have set up this test for encyclopedias to fail from the start as encyclopedias aren't meant to communicate important ideas among scholars. You could say that encyclopedias exist to provide an important reference to students and are meant for their use.
Incidentally, from the years 1996 to 2006, there have been 12 papers in Web of Science that cite Wikipedia.