For the Refit, to give you an example of the sizes of these models, you get the following lengths, based off of 305m for the "real" Refit:
1/350 - 34.31" / 87.14cm
1/1000 - 12.01" / 30.5cm
1/2500 - 4.8" / 12.2cm
For the most part, I'd argue that it depends on several things, but the foremost for the majority of folks it's display space versus the different ships you'd want to have on the shelf. If you only want one or two models that look impressive and have the display space, go with the 1/350, as you can pack a boatload of detail in one of those babies.
If you want to allow for more than one StarFleet ship, for instance, that has a very nice amount of detail, go with the 1/1000 scale. You can have a decent sized number of ships on your shelves at this scale.
If you want to have a fleet of ships and/or just show off as many of the canon and/or non-canon ships as you can put on a shelf - and don't have issues of Male Inadequacy - then 1/2500 scale is a great choice. There are a large number of different model kits in this scale right now. You can have an insance number of ships on your shelves, showing off entire fleets at one time.
From what it sounds like, tho, you'll want 1/1000 or even 1/1400 scale for your Trek ships.