To determine what to charge:

• Take a look at your competitors' media kits and see what they offer
  
  • How does your traffic compare to theirs (how much and where from)?
  • How does your content compare to theirs (quality and quantity)?
  • How does your design compare to theirs?
  • That should give you somewhere to start from.
• Take a look at your AdSense earnings:
  
  • What is your current eCPM (effective cost per thousand impressions)?
  • For most sites I would double your AdSense eCPM as a guide of what to charge.
• Variations
  
  • Different ad sizes would give different CPMs, with larger formats worth more.
  • Ads above the fold are generally worth more than those below the fold.
• Your Media Kit
  
  • Don't make it too complicated with too many options
  • Show your stats (possibly with graphs)
  • Show your rates for each ad size
  • Show any discounts you have for bulk buys
  • Show all your contact details (email/phone/address)

Things to look for when doing a direct ad deal:

• Research the advertiser
  
  • Try to make sure they are legitimate and reliable
  • Get some good contact info on them (phone/email/physical address)
  • Make sure you know which individual you are dealing with for the advertiser
  • Maintain good relations with the advertiser throughout the deal and after it for the chance of future deals.
• Check the ads
  
  • You don't want them to offend your users
  • You most likely want them to fit your site's niche to get a good ROI for the advertiser for a future relationship.
  • Take a look at the ads in the sizes you are running to make sure you like them
• Get both parties to sign a contract
  
  • Impressions/Uniques/Targeting/Time-frame/Ad Serving/Ad Reporting)
  • An advertiser is less likely not to pay you with a signed contract (although that still won't guarantee payment)
  • A good contract won't cost that much and can be used over and over again
• Payment upfront
  
  • The only way to guarantee payment is to get it upfront
  • Ask for at least 50% of the payment of the ad deal up front as a guarantee