I don't know what would be 'the best' application to do this, but for a somewhat basic benchmark tester, check into 'nBench' which can be located on sourceforge.net and elsewhere. It runs 10 different benchmarking tests over a few minutes and produces 3 categories of results. It may not prove anything absolute, but will give you an idea if your configuration or settings have improved kernel efficiency or worsened it.
I use it to check the results of BIOS memory timing adjustments and PCI/AGP timing adjustments.
It's been around forever, updated as required, and is very simple to install and use.
Another way of benchmarking involves using a compiler to compile a relatively large sourcecode, and timing the job while watching CPU usage and memory usage.
Google has many links to Linux Benchmarking apps and sites.