Depending on what size of custom transformer you need micro wave oven transformers and HID type lamp ballasts(Mercury Vapor, Metal halide, High Pressure Sodium, and Low Pressure Sodium) are by far the most versatile and easiest to come by cheaply and take apart and put back together with minimal effort.
The HID ballasts come in sizes from around 35 VA to 1500 VA with 100 - 1000 Va being the most common and are usually two or three piece cores held to together by simple welds along the seams that are easily cut with a hacksaw or small cutoff wheel in a grinder. The best part is they can be put back together with nothing more than a thin coating of JB weld between the seams!