I use the SubInACL utility for this. For example, if I wanted to give the user job on the computer VMX001 the ability to start and stop the World Wide Web Publishing Service (also know as w3svc), I would issue the following command as an Administrator:
subinacl.exe /service w3svc /grant=VMX001\job=PTO
The permissions you can grant are defined as follows (list taken from here):
F : Full Control
R : Generic Read
W : Generic Write
X : Generic eXecute
L : Read controL
Q : Query Service Configuration
S : Query Service Status
E : Enumerate Dependent Services
C : Service Change Configuration
T : Start Service
O : Stop Service
P : Pause/Continue Service
I : Interrogate Service
U : Service User-Defined Control Commands
So, by specifying PTO, I am entitling the job user to Pause/Continue, Start, and Stop the w3svc service.