Take a look at the com.google.appengine.api.quota package.
It provides the QuotaService interface (with implementation and factory) in several ways to check and monitor Google App Engine quotas.
import com.google.appengine.api.quota.QuotaService;
import com.google.appengine.api.quota.QuotaServiceFactory;
...
QuotaService qs = QuotaServiceFactory.getQuotaService();
long start = qs.getCpuTimeInMegaCycles();
doSomethingExpensive();
long end = qs.getCpuTimeInMegaCycles();
double cpuSeconds = qs.convertMegacyclesToCpuSeconds(end - start);