I don't like to deal with slot motherboards, and I always want an ISA slot for my AWE64 in any W98 machine, so my mandatory choice would be the first one. For the RAM, if I will not build the rig as a XP multiboot one, 512 is more than ok, 1GB will come with its own problems to solve (minor but, well...) without any gain (repeat, as long as there will no XP on the same system). I never overclock any of my systems, retro or modern.
When it comes to my real preferences, but I also choose not to use Celerons, while there is the real deal. Celerons were the cheap alternatives during the days, but today, a real PIII and a similar Celeron (disregarding the rarity of some pieces) doesn't cost any different. So my choice of CPU for a PIII W98 system will be either a 1000MHz Coppermine, or a 1400MHz Tualatin, (according to the motherboards' capabilities). I also like 133MHz FSB and some other features that came with it, so I also choose Via Apollo 133 chipsets over the others.
For the display card, my choice will be a GF2 Ultra or a GF4 Ti4400/4600, supported if possible by a Voodoo2 SLI setup. I will definitely have a NIC (3com 905) and a SCSI controller (Adaptec 29160) for the 73/146 GB data SCSI disk I must have. My IDE channels will have two IDE 80-120GB HDDs, an IDE DVD and an IDE to CF adapter (possibly front panel type, although its relatively more expensive. one of the HDDs will have W98SE, the other one will have MS-DOS 6.22 and W95 OSR2.1/2.5. SCSI disk is for data (ghost images, ISOs, zips, drivers, etc.).A real 1.44 floppy and a Gotek USB to floppy adapter will be good, too. Sound card will be AWE64, preferably gold with SIMMCONN and 32MB RAM.
So:
Tualatin 1400 on a branded board with Via Apollo Pro 133T chipset (Gigabyte?)
512MB PC133 RAM
Geforce4 Ti4600 128MB (Asus?)
Voodoo2 12MB SLI (Diamond Monster?)
Sound Blaster AWE64 with SIMMCONN + 32MB (Gold?)
3Com 3c905 series NIC
Adaptec 21960 Series Controller
120GB IDE HDD (Windows98 SE)
120GB IDE HDD (Windows95 OSR 2.1/2.5 and MS-DOS 6.22 + Windows 3.11- 2GB + 118GB partitions)
146GB SCSI HDD (Data - 2GB + 127GB partitions)
IDE DVD player, burner, etc.
1.44 Floppy
Gotek Floppy emulator
3.5" front panel IDE-CF adapter
USB CF reader
Lara Croft wallpaper
Optional:
A 73/146 GB SCSI for Windows ME/Windows 2000
A Matrox (Millennium II or Mystique 220, preferably with Rainbow Runner) for Windows 3.11
GA-6VTXE PIII 1.4+512MB
Geforce4 Ti 4200 64MB
Diamond Monster 3D 12MB SLI
SB AWE64 PNP+32MB
120GB IDE Samsung/80GB IDE Seagate/146GB SCSI Compaq/73GB SCSI IBM
Adaptec AHA29160
3com 3C905B-TX
Gotek+CF Reader
MSDOS 6.22+Win 3.11/95 OSR2.1/98SE/ME/2000