For all my companies smaller notches we use a simple trick.
Take a piece of 5" pipe(1/4" thick or better), cut a section 3" long. Then cut this section in half to make two half circles. -o- to C
Hold the half circle up to the frame rail making sure the bottom is flush. Mark it all the way around. Next, cut the section out. Then, hold your half circle in the area and clean up your cuts to make a smooth fit easier to weld. Then just weld in your half circle of pipe, both sides: inside and out. this is frame rail so pay particular attention to your welds, make sure you get a good weld.
I've done one and it turned out pretty well. It was for an old trailer frame that we lowered to make a flatbed, so if it held up for one axle and 20,000 lbs, it should hold up for a vehicle.
I simply fabricated and welded the C-notch in place first. I found some 2" x 4" square tubing that matched the profile of the original frame. I cut risers with 22.5* angles top and bottom and a cross piece with corresponding angles. I cleaned off the top of the frame, welded the C-notch in place with a good 220v MIG making sure to get really good penetration, then I cut out the original frame between. The original frame was just a channel, so I firmed things up by boxing the frame about a foot in front and behind the notch
If I do a c notch in a car frame I don't cut any more than half of the height out of the frame without adding something to the top to put the strength back in. I usually add a plate to the inside of the frame that goes about 4 inches on either side of the notch and rosette weld it to the inside of the frame.
This would apply to the cut out and pipe filled method described in post 3. On an F1 channel steel frame the "C" notched section needs to be boxed at least 10 inches fore and aft of the notch if you use the "pipe filled" method.
The "C" frame method like curtis73 described keeps the strength in by design.
check the lowrider companys like Thorbecke Brothers, they sell universal C-notches and specific ones, if you call them they'll build you anything you want. they specialize in air-ride systems for those Mini-Trucks. one of the local garages has been building them and they currently have a built 55 ford pickup, its lowered and tubbed, and has a nice c-notch for $6500. ill get a diagram of a notch for you if i can find the one i had.