It all depends on the county and/or officer. In my experience, cops can almost always find a reason to pull you over in CA for any aftermarket parts. The upside is that you can find shops anywhere here that will install anything (for a price). That "50 state legal" statment you see on most exhaust/intake products does not completely apply to CA. I've even seen cops pull over and hassle guys with C.A.R.B. stickers on their parts.
For the most part, you can change your exhaust pieces after the cats with little to no problems from the law (muffler and Y-pipe, as mustard stated). There's always that cop, though, that will pull you over for having a "loud muffler." Bottom line - get your exhaust done how you want it (keeping the cats) and just don't drive like an idiot.