I swapped three motherboards and made the transition from Intel to AMD using Abit and MSI boards with different chipsets without a clean install. Went for about two years without a clean install of Win98, upgrading to 98sE along the way. I finally was forced to do a clean install recently.
You can use the registry ENUM method or you can just use the system Device Manager. I've never done this with any OS except Win98 or 98SE. Basically:
Boot to Safe Mode.
Open control Panel/System/Device Manager.
Remove EVERY DEVICE except PlugNPlay BIOS and Dial UP Adaptors.
Shut down normally.
Install the new motherboard, ram, cpu/heatsink, floppy, HD, CDROM and video card - thoroughly read mobo manual.
Have all device drivers ready for device detection and driver install.
On startup, immediately enter BIOS and set defaults per your manual. Restart any let the OS detect all devices. Install chipset drivers and video card device driver.
Once that's done, install other devices one at a time, rebooting after each device installation.
Usually, a conflict-free installation is the result. If there are conflicts, they can usually be resolved by an overlay install of the OS (just install the OS on top of itself - same directory).
Clean install + download of all updates is really the best way. But reinstalling all apps and tweaks and tweaking is really a week-long project. My way takes about 30 minutes, and the registry maintains all installation/configuration data - even if you're forced to do an overlay install of the OS.
Hope this helps!