A system for debugging targets using various techniques, some of which are particularly useful in a multithread environment. These techniques include implementing breakpoints using out-of-line instruction emulation so that an instruction replaced with a breakpoint instruction does not need to be returned to its original location for single-step execution, executing a debugger nub for each target as part of the target task but using a nub task thread for the nub execution that is separate from the target task threads, providing immunity from breakpoints for specified threads such as the nub thread via specialized breakpoint handlers used by those threads, and virtualizing the debugger nub such that a shared root nub provides a uniform interface between the debugger and the target while specialized nubs provide differing functionality based on the type of target being debugged.