I usually put them under the frame rails just in front of all the steering linkages and all. Don't know if that's a good idea, but the LCA's aren't very suitable due to the grease fittings (and a bad idea when working on suspension parts in general).
In the rear you can use the axle for it I guess.
To lift the whole front I use the bottom of the radiator support... which is now difficult with the addition of the tranny oil cooler (we routed the lines through there). For one side only (like removing wheels/tires, for brake inspection/work, etc) I lift the LCAs. For the rear I lift under the pumpkin. As far as jack stands, I usually just put them right behind the front wheels or just behind the rears (there's a little pad in these spots where the jacks clearly can go).