IMO, the big difference comes in terms of headroom. At low volumes, there may not be a big perceived difference, but once you turn them up I think 50 or 60 watter may thin out a bit more than a higher wattage amp of the same type. AS the headroom of the 50 watter is eaten up and power tube breakup comes into play, I think the thickness or bigness of the tone can suffer. Maybe it's just me, but on any amp that has a "half the watts" variant, I've found I prefer the higher wattage version. The low end seems fuller, seems to have a little more punch, etc. I know with a lower wattage amp you hit the sweet spot sooner and get power tube breakup which many seem to prefer...But for metal, I don't get too much into power tube breakup, as I think it makes the low end a little too muddy or loose, or it just kinda washes out in general. Keeping enough headroom to keep the low end big and clean (well, relatively speaking) is something I'd be more interested in, personally.
That said, depending on the amp, the "big" factor may be there in a 50 watt version...I'm just saying doing some comparos side by side, I think you can usually tell a difference, and to me it's the punch, depth and thickness that you notice with the higher wattage version. At rehearsal a few weeks back, the studio we rehearse at has a couple 800's there, a 50 watt and 100 watt. I asked the owner if I could try them out and the 100 watter just had more oomph and thickness to it...But, the 50 still had enough.
EDIT
My comments I should clarify are based on what I've heard playing them. Whether or not any of this makes any difference in a miked up recording situation I have no clue.