You can use old good hdparm to find out how fast is your hard disk under Linux. There is another tool called Bonnie++ which is a benchmark suite that is aimed at performing a number of simple tests of hard drive and file system performance. Then you can decide which test is important and decide how to compare different systems after running it.
Linux.com has published article about a new tool called fio:
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fio was created to allow benchmarking specific disk IO workloads. It can issue its IO requests using one of many synchronous and asynchronous IO APIs, and can also use various APIs which allow many IO requests to be issued with a single API call. You can also tune how large the files fio uses are, at what offsets in those files IO is to happen at, how much delay if any there is between issuing IO requests, and what if any filesystem sync calls are issued between each IO request. A sync call tells the operating system to make sure that any information that is cached in memory has been saved to disk and can thus introduce a significant delay. The options to fio allow you to issue very precisely defined IO patterns and see how long it takes your disk subsystem to complete these tasks.