Disclaimer: I'm a Clover developer at Atlassian. I see that you've tagged your question with 'clover' so I'm answering :-)
In Clover you can do it in two ways (also combine them):
1) You can define a context filter and do not instrument methods with a cyclomatic complexity <= N. See <clover-setup maxComplexity="NN">
2) You can define your custom metric, for instance multiply coverage value (or better - the 'uncovered' value) by a cyclomatic complexity. Such metric would show complex, uncovered methods as more significant that simple, uncovered ones. See <clover-report> / <columns>
Oh. One more thing. Clover automatically does it for you :-) In the HTML report you can see a "tag cloud" of Top Project Risks metrics which takes coverage+complexity to show the most potentially critical parts of the application.
References: