Look for hidden costs like late processing fees and hotel security deposits. Check your local and national newspapers for reports on the area you will be traveling to. Look for civil unrest, government and monetary issues, travelers' warnings and alerts, and storm watches. Make sure the deposit or portion of the paid trip is fully refundable under these conditions. Make sure you know your deadlines on payments and cancellation policies.
Some companies offer cancellation insurance.
Factor in all taxes for both arriving the country and departing. Certain governments change fees on a 'whim'. Try to place all travel transactions on a credit card. If there are disputes, a credit card company will go after the vendor for the recovery of fees you have paid. I prefer American Express.