Most have a start-up fee + an on-going monthly management fee. However, there are not any "industry standards", you can charge whatever you like.
These are often additional fees because of 3rd party resources the agency is paying.
The way 3rd party apps are paid (pass through cost, agency absorbs cost in pricing, agency adds on pricing variables, etc) can also effect how the pricing looks.
Their business is online merchandising so there are seasonal highs and lows to their spending. In January our fee might appear high, but in December it looks cheap. Overall our fee works out to be something less than 5% of their spend. We deliver a significant volume of their overall traffic, so they are very satisfied.
They spent well over a million dollars this year on search marketing, so my American Express points are huge, but otherwise I don't benefit from their increased spending. However, when they inquired about adding AskJeeves to our program, I told them how I'd raise their fees 30% to capture about 3% more volume and they backed off quickly.
If I were approached by a small client (under $1000 per month), I'd probably have to base my charges on the number of KWs I'd be managing and the likelihood that they would require frequent changes. It certainly wouldn't be 5% of their spend if they had a thousand KWs.
When determining pricing structure, it is important to provide good value. Don't assume that because they are unfamiliar with search marketing, your clients will cheerfully overpay for long. Eventually they will recognize whether they are getting good value or not. Don't count on this taking them very long.