What Programs Work Duing a Jak Sinclair Run
Some programs will still work during a Jak Sinclair run.  The key is the FAQ clarification on "Using":


  Any time an ability is optional, the player resolving the ability is “using” the ability. This includes all paid abilities and all optional conditional abilities (triggered abilities that use the word “may” or “allows”).


So any unconditional triggers on programs will still work.  Here are some examples:


Pawn and Au Revoir work completely (their triggers are unconditional).
Snitch doesn't work (it's ability says "may).
Datasucker and Medium half-work: they will give you virus counters if the run succeeds but their virus counters don't do anything during the run (Datasucker's is a paid ability and Medium's ability says "allows")