Well, it's up to you.
Usually on servers the biggest partition is for /var where stores www, mail and db data.
With 3 harddrives you can keep in mind a RAID 1 (or RAID 5 if is supported by your hardware). It depends if you prefer capacity or security.
If I had this server may be I had used first disk for whole system and second and third for /var in RAID 1.
The best way is configure partitions manually, and the easiest way is all in one partition.
This is my partition scheme for ISPConfig on Debian 6
Filesystem Size Used Avail Use% Mounted on
/dev/sda1 14G 346M 13G 3% /
/dev/sda5 9.2G 149M 8.6G 2% /home
/dev/sda8 7.4G 145M 6.9G 3% /tmp
/dev/sda6 14G 931M 13G 7% /usr
/dev/sda7 184G 35G 140G 21% /var