If the speed problems are primarily caused by rotational speed and you have some extra money to spend ($150), an (inelegant, non-geeky) way to fix it would be purchasing a fast SLC SSD (solid state drive). Got myself the mtron mobi 16GB. Lacking mechanical components the random access properties are obviously quite good. Throughput with Read and Write Speeds of roughly 100MB/s is also decent.

The recommendations of the other monks to use a "normal" dbms such as mysql will probably also result in a decent performance gain.