It depends very much on the nature and size of the business. I would identify major risk areas, such as liability of sales, whether input tax can be claimed, whether the VAT percentage on each transaction is correct. Hope that gives you somewhere to start.
Although not a check to see if the actual VAT Return is correct or not, if the client meets the requirements, I would check whether it may be to the client's benefit to use the Flat Rate Scheme!
My thorough check is data-mining a list by VAT code and visually scan the two-character nominal code on each entry. So if I mine Zero items I will see only transactions for rent, water, travel, food etc, being codes OR, OH etc respectively.
Mining Non-VAT items should only bring up MOT's, Wages, Drawings, OM, OW, DD
Basically it helps you see the wood for the trees. I can double check a hundred items in a minute and an OF code in the Zero items would stand out like a sore thumb - I'd instantly know the clerk has not entered VAT against motor fuel. The client I'm now doing always disclaims VAT on motor fuel, so in this instance it has been entered it correctly.
Then do the same for Standard, Fuel Rate and Exempt. Its slows things down when there's a temporary VAT Rate.
1) Bank balance agrees with statement or rec. 2) Cash is not overdrawn. 3) Fuel Scale Charges 4) Dr or Cr VAT Account 5) EC Lists