If you're still using the 2.4 kernel rather than the newer 2.6, you're more likely to have problems with new hardware. Even parts made as recently as a year ago may be unsupported in the 2.4 series. Such devices include serial ATA (SATA) hard drives, controllers, and RAID adapters, and motherboards based on the nForce 3 chipset. You're also likely to experience a number of serious problems related to Advanced Configuration and Power Interface (ACPI). If you must use the 2.4 kernel, use the latest one, or at very least something newer than 2.4.24.
If you're planning on going with an AMD64 processor and want to run in 64-bit mode, you're much better off with the 2.6 kernel. Mandrake, SUSE, Gentoo, and Fedora Core all have good 64-bit editions for the AMD64 architecture. If you're interested in BSD, both NetBSD and FreeBSD have AMD64 editions as well.
Motherboards and processors
If you're undecided about the old AMD vs. Intel issue, the best "bang for the buck" at the moment is the Athlon 64. Performance in 64-bit mode is far superior to equivalent Intel processors, and the motherboards the Athlons use are generally more feature-rich. The chipset to use is the VIA K8T800, and you'll want to make sure you're buying a motherboard with the right socket -- Athlon 64 processors have 754 pins. Opteron processors have 940 pins; the Athlon 64 FX series has used an identical 940-pin design until the recent release of the Athlon 64 FX-53, which uses a different 939-pin grid array.
Intel's Prescott core is not very effective in the socket 478 package, but the technology will make a bigger impact when Intel introduces products that use the new Extended Memory 64 Technology, which is their own version of the AMD64 instruction set architecture. Put simply, the P4 Prescott draws an enormous amount of power (more than 100 watts) and runs extremely hot (idles at about 60 degrees Celsius under normal conditions), and as a result the stock CPU fan is very loud.
Brand doesn't matter as much as it used to. Intel makes the fastest and most reliable motherboards for Intel processors, followed by Asus and then the rest of the pack. For AMD processors your best bet is probably Asus, but you might find that other brands meet your needs at a lower cost.
Just as with CPUs, the video card debate rages on: ATI or Nvidia? If you're using GNU/Linux or FreeBSD and you want to play games that require hardware 3D acceleration, the best choice is Nvidia. ATI's Linux driver is horrible; it performs very poorly and seems to be missing support for a specific function that Unreal Tournament 2003 and 2004 use. In order to keep those games from hard-locking the system or corrupting the display, you need to turn the graphics detail down to low settings. There is also no support for any of the features of the All-In-Wonder models. Want a 64-bit driver? Forget it -- ATI offers only a 32-bit edition. Lastly, you'll have unfixable problems with ATI's newer graphics cards and distros that use older 2.4 kernels like Java Desktop System, Red Hat Enterprise Linux 3, and SUSE Desktop, among others.
Nvidia on the other hand has excellent high-performance drivers for both 32-bit and 64-bit kernels and even offers an older version of its driver for FreeBSD. (However, I've never actually been able to get the FreeBSD driver to do anything except lock up my system despite using two different video cards, two different motherboards, and a day's worth of configuring and tweaking.)
The newest Nvidia chipsets that are currently available for the desktop market are the GeForce FX series, specifically the 5900 and 5700. The 5800 has been discontinued for some time, but the 5600 and 5200 are still around and available in a variety of configurations. More recently introduced are the 5300 and 5500; I haven't had the chance to test them yet. You'll want the Ultra edition for the best performance, and if possible you'll want to get a card with DDRIII memory instead of DDRII unless you're trying to save some money.
Again, brand doesn't really matter much -- it's all a matter of features (like dual DVI instead of single VGA or dual VGA, TV out, S-Video out, etc.), price, and the Windows software included with it. Reliability seems to be pretty good across all brands that I've tested.
Lastly, keep in mind the fact that most hardware review Web sites are benchmarking DirectX (DX) performance when they rate and review video cards, and that doesn't matter to GNU/Linux users. All we care about is OpenGL performance, and that is not parallel to DirectX performance. The GeForce FX 5600, for instance, gets about the same level of DX8 performance as a GeForce4 TI-4200, but when it comes to OpenGL, the FX 5600 is more equivalent to the greater power of a GeForce4 TI-4800SE. The Ultra edition is even faster.
No doubt, the best desktop hard drive on the market right now is the 10,000RPM Serial ATA (SATA) Western Digital Raptor. In Linux the maximum protocol it can use is ATA-100, even though the SATA standard is faster. It's technically able to go up to 150MB/sec, but that's a theoretical rating. Even ATA-100 and ATA-133 hard drives can't come close to their theoretical maximum transfer rate regardless of which operating system you use, so there doesn't seem to be any problem with using an older transfer standard for SATA drives in Linux. The Raptor is available in 36GB and 72GB models. Both are relatively expensive compared with parallel ATA drives.
Seagate SATA drives aren't terribly impressive in terms of performance, but they're certainly cheaper than the superior Raptor. Maxtor SATA drives are basically the same as their parallel ATA drives but with a different interface. If you're looking for a 7200RPM SATA drive, Maxtor is probably the best choice for performance and reliability right now.
DVD writer prices have plummeted in recent weeks, mainly due to market saturation and the expanded availability of drives that support both the + and - standards. The future of the technology is to get faster and support writing standards that fit more data on each disc. If you don't mind a slower drive you can easily pick up a DVD writer for less than $100; it makes an excellent backup device for your /home directory or OGG collection. If you want to go top-end, look for something that will write dual-layer DVDs -- Sony's DRU-700A is a good choice.
Keyboards and mice
No matter what you think of its software or business practices, Microsoft makes excellent peripheral hardware. I recommend one of the desktop packages that bundle a keyboard and a mouse together, unless you're particularly attached to your current keyboard or mouse. The Microsoft Wireless Optical Desktop Pro includes an improved version of the Microsoft Natural Keyboard and a Wireless Intellimouse Explorer. If you're looking for a "straight" keyboard design or if you're more of a gamer than a typer, Logitech's Cordless MX Duo is an excellent choice.
The only downside to new keyboards and mice is that you can't use any of the fancy buttons and features that are software-driven -- the required software only works with Windows. That means no multimedia controls, no extra mouse buttons (aside from the usual two plus the scroll wheel), and no application-specific or Internet buttons will work in GNU/Linux. Will cordless products work? Of course -- they're all USB or PS/2 (with the exception of one or two Bluetooth products), so the kernel doesn't know (or care) that you're using a wireless mouse instead of an older corded model. As far as the OS is concerned, it's just another input device.