It depends on what type of quilt I'm making. If it's one with lots of matching seams, points, triangle units etc. then I generally will use aurifil 50 wt 2ply since that gives me a more accurate quarter inch seam than other thicker threads.
If it's an improvisational piece, I tend to use whatever works with the fabrics I'm using and I don't worry about getting a precise seam allowance since it's not necessary.
Rob