Use the built-in schtasks command to create and manipulate Windows tasks (basically the equivalent of *NIX cron jobs).
If a task points to a file that you’ve obtained write access to, then that file can be altered without changing the underlying task.
It may also be possible to create your own tasks.
Stealthy tasks
How to hide Windows tasks using PsExec
Deleting the task Security Descriptor will make the task invisible to any user in the system. Note that this requires PsExec!
Use PsExec64.exe -s -i regedit to open regedit with SYSTEM privileges.
Search in HKLM\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Schedule\TaskCache\Tree\ for the task to hide. Under the key for that task, there will be a value named SD that contains the security descriptor. Simply delete it.