There are three types of average, and what you are originally using is the mean - the sum of all the values divided by the number of values.
You might find it more useful to get the mode - the most frequently occuring value:
select name,
(select top 1 h.run_duration
from sysjobhistory h
where h.step_id = 0
and h.job_id = j.job_id
group by h.run_duration
order by count(*) desc) run_duration
from sysjobs j
If you did want to get rid of any values outside the original standard deviation, you could find the average and the standard deviation in a subquery, eliminate those values which are outside the range : average +- standard deviation, then do a further average of the remaining values, but you start running the risk of having meaningless values:
select oh.job_id, avg(oh.run_duration) from sysjobhistory oh
inner join (select job_id, avg(h.run_duration) avgduration,
stdev(h.run_duration) stdev_duration
from sysjobhistory h
group by job_id) as m on m.job_id = oh.job_id
where oh.step_id = 0
and abs(oh.run_duration - m.avgduration) < m.stdev_duration
group by oh.job_id