An ISR (Interrupt Service Routine) and IST (Interrupt Service Thread) are two Interrupt Mechanisms that are used to handle interrupts in Windows CE that are also to referred to as Bottom Half and Top Half Interrupt Handlers.
In the majority of cases, a Windows CE driver will never have a real ISR, and will instead only have an IST. There are of course exceptions to this such as Interrupts that MUST be shared along with Interrupts that have a more time critical approach.
An ISR is not required in Windows CE as the OAL's Interrupt Handler should automatically cause an IST to unblock if no ISR is present for an actual Interrupt. Because of this, drivers that do not require the functionality that an actual ISR provides may simply create and use an IST instead.
Interrupt Service Thread
An interrupt service thread is basically a thread that has an infinite loop around a call to WaitForSingleObject that uses a special "Windows Event" to wait against. The call to WaitForSingleObject will unblock when the SYSINTR that this event is initialized against is returned from the OAL Interrupt Handler.
Interrupt Service Routine
This is commonly referred to as an "Installable Interrupt Service Routine" when dealing with Windows CE. This is created and loaded by the Driver to do some early processing on behalf of the driver.
Most commonly, these drivers are used to do memory copies from hardware to a software buffer, or to enable the use of Shared Interrupts.
MSDN: Installable ISRs and Device Drivers