Kiosk: A Magazine of Literary Journalism
Princeton Journal of Bioethics
BIOS: A Quarterly Journal of Biology
American Scientist
Journal of Young Investigators
Essays in Medieval Studies
Aporia
Codgito: Memorial University Student Journal of Philosophy
Cyberphilosophy Journal
Epistemi
Janua Sophia
Meteorite: Student Journal of Philosophy from the University of Michigan
The Dualist
Journal of Psychology and Behavioral Sciences
Journal of Psychological Inquiry
MarSci: Online Journal for Undergraduate Research in the Marine & Aquatic Sciences
Michigan Journal of Political Science
Issues in Political Economy
The Allegheny Review
The Catalyst
Kaleidoscope: University of Kentucky Journal of Undergraduate Scholorship
UC Riverside Undergraduate Research Journal
Chrysalis: The Murray State University Journal of Undergraduate Research
Explorations: The UC Davis Undergraduate Research Journal
Washington University Undergraduate Research Digest
The Undergraduate Economic Review
Ivy Journal of Ethics
Yale Journal of Biology & Medicine
SIAM Undergraduate Research Online (SIURO)
Stanford Undergraduate Research Journal

The Council of Undergraduate Research also has a list of undergraduate research journals on their Web site:
http://www.cur.org/resources/students/undergraduate_journals/