Aside from the fact that The Bush tax cuts, Welfare reform, and The Balanced Budget Act of 1997 went through reconciliation:
NPR's Julie Rovner has a fantastic article explaining that the reconciliation process has actually been used for almost all major pieces of health-care legislation passed over the past 20 years. COBRA -- which stands for the Consolidated Omnibus Budget Reconciliation Act of 1985, but has come to mean the much-beloved program that lets you keep your health insurance when you lose your job -- was done in reconciliation. The Children's Health Insurance Program was done in reconciliation. The Emergency Medical Treatment and Active Labor Act, which is the legislation that tells hospitals that take Medicare and Medicaid that they have to at least screen any patient who enters the emergency room, regardless of insurance status, was done through reconciliation. Welfare reform, which disentangled Medicaid from welfare, was done in reconciliation.
Need I go on?
Elsewhere, political scientist Joshua Tucker found a Congressional Research Service report (pdf) listing every time reconciliation was used between 1981 and 2005, and he built a rough model testing which party used the process more frequently. During that period, there were 19 reconciliation bills, 11 of which were signed by Republican presidents, five of which were signed by Democratic presidents, three of which were vetoed by Democratic presidents, and none of which were vetoed by Republican presidents. "By my admittedly simple classification scheme," Tucker concludes, "this would suggest that 14 of the 19 times reconciliation was used between FY1981 - FY2005, it was used to advance Republican interests."
http://voices.washingtonpost.com/ezra-klein/2010/02/the_recent_history_of_reconcil.htmlIn addition, you are correct: reconciling the Senate and House bills is exactly what the process was intended for.