Here in Washington State cars and pickup trucks get emission testing on a Dyno with a tailpipe sniffer. We are tested for NOX, unburned Hydrocarbons, and % C02. As DrGallup mentioned, if you fail there is a cap on the amount you have to spend on repairs (I think it's $200) Our standards are lower than California, but in a couple of years we are ramping up to California levels.
The real reason they don't test bikes is economics. The dynos they use for cars wouldn't work for bikes. The State isn't about to invest in specialized dynos for 3-5 % of the vehicles on the road, so they just exempt them from testing. However, there's plenty of cars out there with aftermarket exhaust that are passing the test so I don't think most bikes are in any danger if they should start testing.
I have all my factory stuff except for the pre-cat so I'm not worried. If necessary I'll take it into my dealership's dyno and build a custom map via Tuneboy that WILL pass DEQ. Then take 20 minutes and tear all that crap off again. :eboy: