ISA are older than PCI. ISA stands for Industry Standard Architecture. There is another type of old slot called EISA (Extended ISA). ISA slots were on the very first IBM PC!
Making cards to plug in to ISA is much (really, much) simpler, but not many (any?) modern PC's have them. You are most likely to encounter them on emdedded PC boards these days.
PCI slots can transfer data much faster, share irq's and resources, take control of buses and are designed to work better with modern operating systems. They are also practically impossible for amateurs to make boards for
I have read that ISA and EISA cards are not supported in Windows XP. This seems odd since some of the ISA cards are Plug and Play.
Oh well, older motherboards become cheaper faster than new motherboards. I still have a 4.77 MHz 8086 running DOS just because my prototype EPROM burner is EISA. Well, because its EISA and I don't want to put a homemade circuit that uses 21 volts in a computer I actually work with.
ISA is 16-bit bus while PCI is 32-bit bus. ISA is "eating" pretty much of the 64KB of the x86 I/O space while PCI only uses CFCh-CFFh. The bus speed also different. If you are programming for this bus, then the only thing that matter is the protocol of the bus, especially addressing, timing, etc. Look at Mindshare's PCI System Architecture and ISA System Architecture book for more explanations.