I'm pensioning off my 10-years-old home server and replacing it with an Ubuntu 10.04 box. The two storage devices are a Western Digital Caviar Green 2.0TB HD and an Intel X25-M 34nm Gen 2 80GB SATA II 2.5inch SSD (the box has 8GB RAM and an i5 750, if it matters).
I don't care much about boot times (since I don't plan to reboot all that often;-); the main frequent, performance-demanding task will be (re)building large open source C or C++ software packages from sources (as an open source contributor, I do that often).
So, I thought I'd keep the SSD as the secondary drive and the HD as the primary one, using the SSD mostly for the files that can otherwise demand a lot of seeking (esp. in a parallel make).
However, the friendly vendor (perhaps more experienced in Windows systems than in Linux ones) thinks the "normal" way to configure the machine would be with the SSD as the primary drive. I'm pretty rusty on configuring and tuning systems, so, I thought I'd better double check on SuperUser... thanks in advance for advice about this choice!