Efficiently projecting datasets of varying coordinate systems into one coordinate system?

Sounds like any way you slice it, either you specify the transformations individually or you don't. Instead of hard-coding things or using ModelBuilder, create a lookup table or spreadsheet (CSV files work well with both Excel and Python) with the datasets and transformations and loop over it programmatically.

I think that in this kind of situation, a real programming (/scripting) solution really starts to shine. For these kinds of analyses (all my analyses actually :)) I use R. It has support for reprojection of data through the proj4 projection library. I suspect that reading and reprojecting the data could be done in under 20 lines of code. Key packages are rgdal for reading and reprojecting data and sp for spatial objects in R. For more detail I refer to the R Task View for spatial data.