• National Science Foundation Graduate Fellowships
  Deadline: November 19th
  The NSF GRFP aims to ensure the vitality of the human resource base of science,
  technology, engineering and mathematics in the U.S. and to reinforce its
  diversity. This fellowship offers a stipend of $30,000 a year for three years
  and a $10,500 cost of education allowance for students at or near the beginning
  of their graduate studies. U.S. citizens, nationals, or permanent resident
  aliens are eligible to apply. For additional program information, go to:
  http://www.nsfgrfp.org/. For application and deadline information, go to:
  http://www.fastlane.nsf.gov.
• National Physical Science Consortium Graduate Fellowships
  Deadline: November 30th
  NPSC's goal is to increase the number of American citizens with graduate degrees
  in the physical sciences and related engineering fields, emphasizing recruitment
  of a diverse applicant pool including women and minorities. The NPSC Graduate
  Fellowship is open to all American citizens; lasts for up to six years; provides
  an annual stipend; covers tuition; and includes one or two paid summer
  internships with a government agency.
• Hertz Foundation Graduate Fellowship
  Deadline: November 2nd
• Ford Foundation Fellowship
  Deadline: November
• National Defense Science and Engineering Graduate Fellowhip
  Deadline: December 14th
  The National Defense Science and Engineering Graduate Fellowship Program (NDSEG)
  The fellowship program is sponsored by the Army Research Office, Office of Naval
  Research, Air Force Office of Scientific Research and the DoD High Performance
  Computing Modernization Program This program is intended for U.S. citizens at or
  near the beginning of their graduate studies in science and/or engineering
  programs. The fellowships are for three year tenures. The stipends begin at
  $30,500 for first year fellows, $31,000 for second year fellows, and $31,500 for
  third year fellows. Full tuition and fees and a health insurance allowance are
  included as part of the program. The application cycle is from September to
  January.
• Office of Science Graduate Fellowship Program
  Deadline: TBA
  The Department of Energy (DOE) Office of Science Graduate Fellowship ( DOE SCGF)
  program supports outstanding students to pursue graduate training in basic
  research in areas of physics, biology, chemistry, mathematics, engineering,
  computational sciences, and environmental sciences relevant to the Office of
  Science and to encourage the development of the next generation scientific and
  technical talent in the U.S. The Fellowship award provides partial tuition
  support, an annual stipend for living expenses, and a research stipend for
  full-time graduate study and thesis/dissertation research at a U.S. academic
  institution for three years.
• Science, Mathematics, And Research for Transformation (SMART) Defense Scholarship - Deadline: December 14
• National Center For Environmental Research Fellowships
  Deadline: deadlines usually November, check the web page
• Department of Energy Computational Science Graduate Fellowship
  Deadline: January 8th
  http://www.krellinst.org/csgf/
  The Department of Energy Computational Science Graduate Fellowship (DOE CSGF) program provides benefits and opportunities to students pursuing doctoral degrees in fields of study that use high performance computing to solve complex science and engineering problems. DOE CSGF participants use math and computers to conduct doctoral research within a broad array of fields,
  including Earth Sciences.
• NASA Student Researchers Project
  Deadline: TBD, approx. February 1st
• NASA Earth and Space Science Fellowship
  Deadline: TBD, approx. February 1st
• ASEE maintains a web page with information and links on many graduate fellowships
• NSF East Asia and Pacific Summer Institutes
  Deadline: November 8th
  The National Science Foundation East Asia and Pacific Summer Institutes for U.S.
  Graduate Students (EAPSI)
  This program is intended for U.S. citizens or permanent residents who are
  graduate students enrolled in research-based science or engineering programs.
  The duration of this summer fellowship is about 8 continuous weeks and research
  is performed at a host institution in Australia, New Zealand, China, Japan,
  Korea, Singapore, or Taiwan. A $5,000 summer stipend, cost of living expenses,
  and round-trip airfare are included in the award. The application cycle is from
  September to December.
• Society of Exploration Geophysicists Foundation Scholarship Program (open to both US and non-US citizens) - Deadline: March 1st
• GSA graduate research grants
  Deadline: February 1st
• Society of Economic Geologists graduate student fellowships
  Deadline: March 1st
• AGI Minority Participation Program
  Deadline: March 15th
• Colorado Diversity Initiative
  Deadline: 4 weeks prior to travel
• Scholarships for women in oceanography
  Deadline: December 6th

Advice on Applying to Graduate Fellowships

Advice on applying for GSA graduate research grants

Note: Deadline for these programs are usually in Oct. or Nov.