its most effective to work out each muscle group once to twice a week. that way you get to recover. a lot of studies say that 48 hours is sufficient to recover but most bodybuilders or just people weight training do each muscle group once or twice a week, which gives the best results
also, each muscle should be trained a certain amount to make sure its properly trained. but if you train all your muscles in one workout it means you're going to go over 1 hour for ur session. some say train no longer than 1 hour. others say 1.5 just find what works for you. i dont know the reason why you don't train longer than that, its got something to do with your body releasing chemicals which does more damage than good.
so what is the solution if you have a time limit and you must give each muscle the right attention? you have to create a 'split' which focuses on certain muscles each session.
pick muscles that work together for each session, e.g. pulling muscles (back and bis) and pushing muscles (tris and pecs). think along those lines.
ive seen posts from a few people on these forums who know what they're talking about. they can give you some more reasons or even correct me if im wrong. i use to know it inside out about 5 years or so ago but forgot a lot of it now, i just know what to do, but can't remember why im doing it