Q1) Opteron 2xx
Q2) DUAL CPU however thier is a QUAD Opteron with AGP coming so be aware and it wont be cheap around the price if a fully configured DUAL ITANIUM.
Q3) SCSI RAID 5 with adaptec controller, linux was originaly for SCSI.
Q4) AMD chipset in the Opteron case the 8000 series.
Q5) Definetly nvidia based card, a geforce 4/5 and preferably a quadro but the 4600/5900 will be fine.
Q6) Depends on your design, iam not sure how linux can use over 4GB of RAM in a 32bit OS. I suggest 1GB DIMMS DDR 400 Reg ECC ($390) and if capacity becomes a problem then 2GB DIMMS DDR 400 Reg ECC ($999) both from crucial. Dont skimp on memory its cheap nowadays and if you have to cut back on something to have more memory then drop the CPU speed. Unless your running 64-bit linux 4GB will be your limit and even then with 64-bit linux and 32-bit applications (i.e. IC 5) you wont be able to have more than 4GB per thread.