Well, apparently Windows doesn't think so lol. The Winx score is not something I get concerned about, and if you are happy with the system's performance, leave it alone. You can probably improve boot times, paging, game load times, and maybe relieve some game "hitching" by going as far as an SSD (an SSD will get you something like 6.4 to 7.4) - but its up to you whether the effort is worth it.
I don't care about the benchmark. However, if I can improve system performance by flipping a configuration setting, installing a newer driver or replacing a relatively cheap storage device, then I would like to.
If everyone is running 7200 Barracudas and getting 3.9, then great. If not, then I want to figure out what's going on.
Most current 7200 RPM drives score about 5.5->5.9 (WEI). When the segate -11 came out they were good performes, (Many had Quality issues). The newer drives have a higher platter density, that means that a sector is smaller and more data is read in a given amount of time. Another factor is Cache, some of the newer drives have more cache and the is used better.
As to the Benchmark itself, WEI is not the best, But a HDD with a score of 5.8 is goinging to be better than one with a score of 3.9. How much of a difference in day-to-day operation - UNK and depends on usage.
As to tweeks, You can enable write caching (if not already enabled), Bear in mind that if you have a sudden power failure, or BSOD, that what ever is in the cache is lost.