I'm not sure there is much, if anything, to worry about in terms of performance. I'm sure someone else will pitch in with some comments on this.
To me your biggest choice would be how to partition the hard disks, but most people just have /boot /(root) and sometimes a separate /tmp so that it can be mounted in a slightly more secure way (see below).
The size of your swap partition is also open to debate. 1.5 times the installed ram, twice the installed ram, the same as the installed ram etc etc. It doesn't really matter all that much as long as you have a good amount of Ram to start with (1Gig is good, more is better) for what may be a busy system.
Redundant hard disks are, in my opinion, also essential, and ideally done via a hardware raid controller. At the very least RAID5 (but probably not if you use software rather than hardware raid as software raid 5 can slow things down a lot according to some people), but mirroring is even better if you can afford the loss of 50% of your disk space. On a new system that we have just put online there is room for 4 2.5in 10k SAS hard disks. In the end we went RAID5 with this, but if we could have afforded larger drives we'd have gone RAID10 which would have given performance advantages and redandacy at the expense of 50% loss of hard disk space due to the mirroring. It breaks my heart really: On the workstations we have in the office we use 4x 500Gig drives in a raid10 configuration with software raid. That still gives us 1TB of disk space. But on a 1U server, with SAS rather than SATA drives, that's just not physically possible let alone affordable.
But I digress....
With a new install you may want to optimise for security more than anything else I think.
Here is a good place to start:
http://www.web-hosting-control-pane....php/HOW-TO_setup_a_PLESK_Dedicated_Server/6/
Faris.