My initial freighters are designed around one standard size cargo hold and 3 size 60 engines. I normally deploy them in fleets of 5 freighters so they carry as much cargo as one freighter built around a large hold. The advantages are the flexibility to perform multiple small deliveries, quicker partial loading time (see bug
http://aurora2.pentarch.org/index.php?topic=11565.msg136403#msg136403 ) and most importantly small jump size. Keeping the freighters and colony ships under 40K tons means the jump engines on my jump tender/jumpgate construction ships don't have to be enormous to allow me to begin setting up a colony on a system before the jump gate is finished.
Plus it lets me use a smaller shipyard to do refits/rebuilds when drive tech improves.
I do have the disadvantage of requiring more operating overhead, especially since I rarely break the freighters out of their 5 ship groups, so other than the special cases outlined above one large freighter would work just as well. I haven't gotten far enough in C# to do so but in VB I'd assign a freighter to larger colony systems to shuttle minerals and infrastructure around as needed instead of sending a fleet from Sol for each job.