On a VA loan, there are certain costs that the Veteran cannot pay, but any other party to the transaction can pay - including the seller. Those fees the Veteran cannot pay are typically called "non-allowables". The only way to get the seller to pay for the the non-allowables is to negotiate it in the purchase contract. If you and the seller did not both agree that the seller would be paying for the Veteran's non-allowables, then another party (real estate agents, mortgage lender, mortgage broker) will need to pay for them.
Chapter 8 of http://www.benefits.va.gov/warms/pam26_7.asp
is the chapter of the VA Lender's Handbook that goes over "Fees and Charges the Veteran-Borrower CAN Pay" and "Fees and Charges the Veteran-Borrower CANNOT Pay"
VA allows a 1% origination fee.
A list of fees that the Veteran typically CANNOT pay, this is *not* all-inclusive:
attorney fees (other than for title), brokerage fees (charged by a real estate agent/real estate broker), prepay penalties, "closing" or "settlement" fees, doc preparation, underwriting, loan application, admin or processing fees, interest rate lock-in fees, notary fees, tax service fees, and termite inspection fee.
Some of those fees still need to be charged though - for example an underwriting fee has to be paid to the lender who is underwriting the loan. So what VA permits is to convert the "non-allowables" to an "origination fee" if it does not exceed 1% (thus the 1% Origination fee that VA allows), which is why often on a VA loan you'll see a higher origination charge when the lender is paying all of the VA non-allowables (vs. a lower origination charge if the seller is paying the non-allowables).
A list of fees the Veteran typically CAN pay, this list is *not* all-inclusive:
appraisal fee, VA compliance inspection fees (if required by the NOV, not if otherwise required by the lender), recording fees, transfer taxes/stamps, credit report fees, pre-paid items (such as pre-paid interest, property tax & homeowners insurance reserves for the escrow account), insurances (flood, homeowners, etc.), well/septic inspection fees, surveys, title insurance/exam/policy, certain endorsements to the title policy, VA funding fee, termite report (on a refinance) amongst others.