This notch you write of is called a rabbet (assuming I understand what you mean). Using a dado blade on the table saw would be the best for repeatability in this instance. Attach a block of wood to your rip fence so you don't damage the fence. Cut the end grain on both sides first to prevent tearout. See pages 8-14 (especially figures 3-40 and 3-41) of the following link: http://www.shopsmith.com/academy/tblsaw_joinery/090902.pdf
. For the size of the stock you are using, I would most likely use the method seen in figure 3-40.
If you don't have a dado blade and cannot buy one. A router with a straight cutting bit and a clamped straight edge can be used as well, you'll either have to reset the straight edge for every cut (time) or you'll have make a jig (time +money).
Finally, if you don't have a dado or router, you can use the normal table saw blade to make multiple cuts in each rabbet, nibbling away at the wood you want to remove, one sawblade width at a time (very time consuming)