What is the best way to merge large files (40gb+)

Yes, NTFS will handle those files. Maximum size of a file on NTFS is 16TB. Source: http://en.wikipedia.org/wiki/NTFS#Limitations

On Windows/DOS you can do copy /b filename1 + filename2 outfilename

On UNIX/Linux you can do cat filename1 filename2 > outfilename

Files of that size should be fine on NTFS

EDIT: You ask in your comment how to do wildcard copying. You can use wildcards in both cases.

On Windows/DOS you can do copy /b *.txt + *.dat outfilename

On UNIX/Linux you can do cat *dat > outfilename