Super popular amongst, well, benchmark whores (there's just no nice way to say it), it's become a favorite application for the bragging rights crowd. But aside from boosting your geek cred and leveling up your Obnoxious skill-set, Super Pi, currently in version 1.5, makes for a handy benchmarking tool and plays double duty as a stability tester. The focus here is on both the CPU and RAM, with tweaks to either one affecting your Super Pi calculation times (lower is better). To gauge performance, I recommend running the relatively quick 1M test, and the much longer 32M benchmark for stability. Just don't post your scores on the forum afterwards, followed by OMGBBQ LOL mY score r0xoRs y0!
HD Tach, as its name implies, measures your hard drives performance, and can handle RAID arrays too. Just be careful with this one, as the synthetic numbers used can insinuate a much larger performance boost than you'll actually notice in a real world setting. For example, a RAID 0 array will destroy a single hard drive in HD Tach, and while RAID 0 is indeed faster, you're not going to notice a night and day difference as would seemingly be portrayed in an HD Tach run.
For all intents and purposes, single core computing is dead. Dual-core CPUs can now be picked up for under $100, and even quad-core has moved into mainstream pricing (Q6600 anyone?). And as far as our benchmarking programs go, Cinebench does a good job of measuring your multiple core processor's performance. You can test your videocard's OpenGL performance too, but I use this one solely for the CPU.
Most games come with built-in benchmarking tools, and some even have real-time FPS counters, but FRAPS works with just about any game. It's not a very good way to compare performance because, without a pre-scripted demo, you can't eliminate uncontrollable factors, such as the amount of animations on a screen, whether the path you took this time was more graphically demanding than the last, and so on. But it is a neat utility for those curious about their GPU's frame rates at any given time, as well as keeping an eye on the real-world performance.
Final Thoughts
There are other benchmarks out there, and how many or how few you choose to run is completely up to you. There's no right or wrong way to go about it, so long as you're confident that your gamut of benchmarking is providing you with sufficient information about your system tweaks. Or you may choose not to benchmark at all, but like pieces of flair, I'd recommend at least trying some out.