If the system has VLB slots that you would like to use, then you want to go the DX4 100MHz route. The reason Intel abandoned the DX 50MHz (so I've been told) is that other chips weren't always reliable at a 50MHz bus speed, though shortages of the DX 50MHz may also have contributed to poor adoption. Getting VLB cards to run at 40MHz can be a task and usually requires using 1 wait state. 50MHz may be out of spec for a lot of VLB cards.
If it's a Socket 3 board with PCI, then any bus speed above 33MHz will result in an overclock of the PCI bus, and a 50MHz bus speed is likely to be too extreme of an overclock for 32-bit PCI devices.
If you only plan to use ISA, then by all means go for the DX 50MHz. (I'd try it at that speed, if I had the processor.) You'll probably have to experiment with the ISA clock divider to find a speed all of your cards are stable at. If you're lucky, maybe you'll still be able to pick a divider of 4 or 5 (some ISA cards are happy at 10MHz or 12.5MHz). But you may have to use a divider of 6, which would result in an ISA bus speed of 8.33MHz, and most ISA cards that would feel right in a 486 will be happy at that speed.
