Some useful sources for scientific papers related to GMOs include:
ICGEB provides bibliographic updates of scientific papers on a variety of issues related to genetic engineering. The website can also be searched.
PubMed (a service of the National Library of Medicine) can be searched for scientific papers in various ways (keyword, author etc.). The site is useful for finding papers related to medical/health issues and is comprehensive. Abstracts and some entire papers are linked to the search results.
AGRICOLA (USDA Library) is one of the best sources for agriculture-related scientific papers on genetic engineering, but does not provide links.
Highwire (Stanford U.) provides links to abstracts and some papers, similar to PubMed. Less comprehensive, but includes more applied agricultural coverage.
Sources of information critical of GE:
AgBiotech Info (maintained by Benbrook Consulting)
AgBiotechNet (subscription required)
Council for Responsible Genetics
The Center for Ethics and Toxics
Industry sponsored sites:
Biotech Knowledge Center (Monsanto's site)