For general fitness and endurance, 25 minutes, six days a week would be better. The best advice I've ever seen for running is: Run. Run lots. Mostly slow, sometimes fast.
One of the best programs I've seen for running comes from a triathlon and cross country coach that I've talked with a few times, and it's 3:2:1. Say your longest run is 30 minutes. You should have 3 runs of 10 minutes, 2 runs of 20 minutes and one run of 30 minutes, with one rest day. The generally accepted way is short, medium, short, medium, short, long, rest day.
This gives you a very solid aerobic base, doesn't overstress you and allows time for recovery. You can work up in time, although unless you are planning on competing, I wouldn't see much need to progress past the 20:40:60 minute range.
The nice thing about general cardio fitness is that it's as simple as getting out there and getting the work in. Almost any plan (such as your 6x25 or 3x50) can work, I usually recommend 3:2:1 as it is simple and extremely effective.
It also works if you are planning a weightlifting regimen, as you can couple the majority of your lifting days with the 3 short runs without being too time compromised.
Edited for ivo's comment below:
On this plan, you would still have to work up to hour runs, if you aren't capable of it currently. So if your long run capability is currently 45 minutes, then you would have 3 runs of 15 minutes, 2 runs of 30 minutes and 1 run of 45. Do that for a couple of weeks, then increase your base time by a few minutes, so you'd be doing 17, 34 51 minute runs, and so on until you reach your goal long run time. You take your current long run time, and work backwards for the medium and short runs.