It all depends on the chipset. Intel was pretty rigorous in dumping legacy from 1999 onwards, so there is no full ISA bus present on the 800-series chipsets. Only way to get an ISA bus there is with a bridge chip. Other chipset vendors such as Via kept an integrated PCI-ISA bridge in their southbridges for a few years longer. Look up the datasheet of the southbridge on the motherboard you are considering, if it has an ISA bridge built in "all" you need to do is to connect the relevant pins to an ISA slot or peripheral.

Practically speaking though there's no difference between a PCI-ISA bridge integrated into the chipset and a discrete one (as long as the latter also supports DMA). A more generic, practical solution one could imagine is a PCI-ISA bridge on a PCI card, that then connects to an ISA backplane. You could make one with three slots that would fit into a standard ATX case below an uATX motherboard. Then stick the card into that slot and hey presto - 3 ISA slots in a more modern uATX system.

Note that a lot of stuff that talks to ISA can be speed sensitive, so although you could this way add ISA slots on anything with a PCI slot, it's unlikely to work well if you get too ambitious with Core i7s and the like.