There should be no hidden charges on your contract. What to look for:
Taxes and surcharges -- there are several of these, so if you are not sure, ask the agent to explain each one
Assessments -- if you use an off-site rental company, you may be assessed a fee for using their shuttle to take you to/from the airport
Things to avoid:
Pre-paid gas -- while they may quote you a slightly less expensive per gallon rate, you actually pay for a full tank of gas. Unless you can return the car practically empty, you are wasting money.
Insurance -- contact your car insurance company to find out what coverage you have when renting (usually the same as your policy). Also check with your credit card company to see if they provide any additional coverage.
I normally decline ALL rental car insurance. It's overpriced and not worth it. Easy way for the agent to jack up their commission.
Upgrades: Agents try to sell you on "cheap" upgrades that end up being very costly. Before agreeing get the low-down on the TOTAL cost of the upgrade, not just the per-day rate.