CPU: Athlon XP 1800+ 1.53GHz retail box, $110 (computergate)
MB: GigaByte GA-7VTXH+ KT-266A w/ lan + sb, $90 (multiwave)
mem: 256MB CAS-2 150x2 PC2400 DDR, $45 (memorysuppliers, newegg)
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SCSI ctl: Tekram U2W/390F, 32-bit PCI, 80MB/s, $130/$75
SCSI HDD: Maxtor Atlas 10K III, 18GB $160 (hypermicro)
SCSI CD-ROM: ? $80
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video card: ?? $30
monitor: ?? $300
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audio card: ? built-in/SB Live/SB Audigy $0/$30/$60
speakers: ?? $5
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e-net card: ? built-in $0/$10
modem: ?? $40
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case: in-win S500 mid-tower or Q500 full-tower, $45-$75
FDD: generic, $10 (computergate)
KBD: NMB, IBM or comparable, $20
mouse: nice 2-button (eg. Mitsumi PS/2), $5

I am in the process of building a workstation for work; this is what I have in mind:
Update: I built the system and have annotated my notes accordingly.

Athlon Slot-A 700 (or Tbird 700-ish)

The Athlon Classic (pre-Tbird) 700 is affordable ($160-ish), and is the highest clocked Athlon with a 1/2 cache multiplier. The Slot-A Tbird is roughly equivalent in overall performance (3-4% faster), is 20-25% faster for cpu-bound jobs, and is slower for jobs with large working sets that fit into the 512k cache of the Classic but not the 256k of the Tbird. The 700 MHz Tbird is about $160, the 750 $200, the 800 $260. Pick a price. I chose to save on the processor to put toward the disk drive.
Update: I bought the Slot-A Tbird 700, though if I were shopping today (November), I would get a Socket-A cpu instead. The socket A has a better variety of processors to choose from, like the 800 MHz Duron.

Thermaltake Golden Orb cpu cooler

Not the top-of-the-line, but it comes close, is much quieter, and is certainly the most unique in appearance. I dislike a monotonic buzzing in the background. It does look strange, however, unless you're into shiny gold.

Gigabyte 7IXE motherboard

The AMD 750 chipset-based boards outperform the VIA chipsets (even the KT133) in cpu-bound jobs, and I want the two ISA slots. I want to move all my existing hardware to the new system without having to install new drivers. There is also an incompatibility between the KX133 chipset and the Tbird (which shows up especially at higher speeds, and 700 seems to be Ok), thus the 750 is a safer bet.
Update: If I were shopping today (November), I would get the GigaByte 7IXE4, which is the same motherboard but with a socket-A connector. And yes, it still has the two ISA slots :-)

128MB PC100 SDRAM

I picked up some used PC100 SDRAM on eBay. I was planning on 96MB, but would up with 128 instead. I'll live :-)
Update: One of the third-party drivers did not like 128MB, so I've downgraded to 64M. I don't notice any difference in how the system performs, though (running Linux 2.2.6).

Supermicro SC730 case

I was tempted to gor for a full tower, but decided that a huge box did not fit into an office environment well. I had a hard time choosing between three mid-towers, the Supermicro sc730, the A-Pro CS-802, and the PC Power Personal Mid-Tower. I settled on the Supermicro because it is less expensive and is better looking :-) I will have to check which power supply the SC730 uses, only a few 235W ATX power supplies are Athlon rated. (I also like the InWin S500, but I decided it was too small for the cooling needs of the Athlon. The InWin 235W power supply, however, seems to be on the AMD approved list - the Powerman part number is identical to the Fortron part number, which is identical to the ..., which *is* on the list.)
Update: I actually used an InWin S500 mid-tower instead. I bought one at auction on eBay, and the auction company finally shipped it (one month later; it's a long story). I'm rather pleased with the S500, this is my first encounter with the ATX layout, sliding drive rails, removable side panels. The power supply is the Powerman FPS-235GTW, which, judging by the model number, is AMD approved for Athlons up to 700 MHz - perfect!
Update: With an eye to upgrading, I swapped power supplies for a nice Sparkle 350W ATX.

Quantum Atlas V 9.1GB SCSI disk drive

This is one of the top-performing (if not the top-performing) 7200 RPM SCSI drives. The nice thing about it, though, is that it's cool and quiet.
Update: I swapped the Atlas V for an Atlas 10K II, and took home the Atlas V. The 10K II has a sustained data throughput higher than my controller at home could handle, so I'm now using the V at home (which at 29 MB/s pretty much saturates the 40 MB/s UW SCSI channel; I've only been able to achieve 33 MB/s out of the 40), and I'm using the 10K II on my U2W-80 controller.

Tekram DC-390U2W SCSI controller

I alread bought this for my home system, but picked up a used Diamond Fireport 40, and will switch. I like the Symbios (aka NCR) SCSI controller family, they perform well and are well supported by all manner of operating systems.

Toshiba 5701B 12X SCSI cd-rom

This is an old hand-me-down from my home system. It works well, and given how little I use my CD drive at work, maybe I should switch it with the 4X Toshiba in my wife's computer :-)

NMB II keyboard

This is a very nice keyboard which I've bought for myself years ago. It has only one really annoying glitch - it does not have N-key rollover. If you simultaneously press four keys, the third key is sometimes registered only when the first key is released, causing the letters to appear out of order (case in point - "dir ", which, if I type it really fast, appears as "di r" - and no, I tested it, it is not due to my typing, it is reproducible). Otherwise, a nice, quiet, good-feeling keyboard.

Mitsumi PS/2 mouse

I still miss my old boxy little Mouse Systems serial mouse - it was cute (it mimicked the old angular one-button Mac mice), it was small, and it felt great. It's also completely dead. The Mitsumi is also a small, nice-feeling mouse, it avoids the huge size and ugly looks of many of its peers, and is really cheap (as low as $5.60). Though the big advantage of serial mice is that the 16550 serial controller generates one interrupt per 16 bytes of data, greatly reducing the interrupt load on the system. The PS/2 Mitsumi generates 300 per second when moved slowly. (Realistically, my K6-III/400 can handle well over 1500 interrupts per second, so this is not a major consideration, but I would not recommend a PS/2 mouse for a 486).

Video Card - from old system

I have limited choice in this matter - I need to use a particular video card that provides masked live video display, since that is the nature of the work I do.
Update: I ended up using my other Matrox Millennium II card after all (AGP, 8MB WRAM), because I ran into unforseen difficulties getting the old video card working correctly with the new motherboard.

Sound Card

PnP ISA Sound Blaster - from old system
Update: I switched to a jumpered, non-PnP card, which fixed all manner of odd problems with both my Windows and Linux configurations. Sigh.

Speakers

TBD - not important - from old system (if I can find them :-)
Update: I brought in my speakers from home that I never used anyway; at $6, they were the lowest cost ones I could find (now only $3.75 including a built-in AC power adapter!)

Ethernet Card

ISA - from old system

Update: I bought a PCI 100T card for $1 on eBay, and am using it instead.