April 2008: a machine that may serve as a Linux workstation
A Dell Vostro 400 MT costs 549,- € (plus tax and shipping, but on the other hand Dell gives a discount to universities) in Germany. It comes by default with a (high-end!) NVidia GeForce 8800GT graphics card, 3 GB of memory, a 500 GB disk, and a quadcore Q6600 CPU running @ 2.4GHz. If most of your data reside on a fileserver, then you might want to put an additional GB ethernet card (5-10€) into one of the two empty PCI slots.
This machine is very cheap, fast, small, and quiet - we have four of those. But as we ordered them in March they "only" have the 8600 GTS graphics (in practice even a GeForce 5200 is fast enough for coot, O and pymol).
This GeForce NVidia card is quite suitable for crystallographic visualization, but - being GeForce and not Quadro - it does not support stereo. But a 22" TFT monitor (about 250,- €) does not support stereo either.
It is a good idea to switch (in the BIOS) the SATA mode from IDE (the default) to RAID before you install Linux, because this activates the very good Linux AHCI driver and makes the use of the Linux kernel option "irqpoll" unnecessary. (This hint applies to all modern chipsets featuring SATA disks; "IDE", "legacy IDE" and "enhanced IDE" are often not the best setups for Linux - depending on the distribution's kernel - , whereas "AHCI" and "RAID" are good. This option can be found in the BIOS, often under "Integral peripherals" or the like.) It is also a good idea to check in the BIOS if the power-saving option of the CPUs is switched on - it is probably called "Speedstep" or "Intel Enhanced SpeedStep" or the like and should be enabled.
Update: we replaced the graphics card in one of the machines with a stereo-capable Quadro card (I believe a FX 1400) which cost about € 400,-, and have now a stereo workstation for about € 1000,- .
 September/October 2008
The Vostro has changed its model number (410), comes with a GB-ethernet card, and should be ordered with a 8800 GT card. The system that I would order would cost € 699,-, so unfortunately Dell seems to have raised the price significantly.
 February 2009
We purchased 3 identical core i7 940 machines; the CPU represents the second-fastest currently available (after the 965 Extreme). Check out the benchmarks at !
The CPU is a quad-core with Hyperthreading, thus appears to the operating system like having 8 cores. The configuration of our machines (with MSI X58 Pro motherboard, 6 GB memory, large disk, and a cheap NVidia graphics card) was established at http://www.hardwareversand.de (I'm not affiliated with this company but I bought my son's PC there, and he's happy with it). The price of such a machine is slightly below 1000,-€, including sales tax and 20,-€ cost for putting the pieces together.
The BIOS has lots of things that one can adjust; at least the IDE mode should be set to AHCI and the C-states activated. After installing the 64bit version of CentOS 5.2 from DVD we discovered that the RTL8111C network adapter is not well supported by the slightly old installation kernel. So we downloaded (from a different machine ...) one of the kernel (plus kernel-devel and kernel-headers) RPM packages from the site http://people.redhat.com/dzickus (at least version 128) and installed those with the help of a USB stick (we also needed the --nodeps option).
Update: NFS under the -128 kernel does not work well under high load. But there are RTL8111C drivers available at  which I will try.
Update 2: Never got around to trying them but my self-compiled 2.6.27.x kernels work well.
Update 3: The RTL8111 driver from ElRepo (see CentOS#Hardware_support) works really well with the standard CentOS-5 kernels, and I'm using those now.