Because I've had to search on this three times in the last year, I thought it'd be a good idea to document this here, for myself and others. There were a number of important changes that can trip you up from version to version and, if you know which version the changes came in it can be beneficial.
First is a change that affects JSON output, though it's not specifically about JSON. The ColdFusion 9.01 updater (the current base install, at the time of this post) addressed Bug 82980 by removing ColdFusion Debug Output from direct CFC requests. This was only important if you had debugging output turned on in the Administrator, but caused lots of issues when testing ajax applications in development environments that kept that setting on by default.
Unfortunately, Adobe made some changes to JSON serialization that were not only unpopular, but technically dead wrong. They were trying to resolve the treatment of numbers in JSON serialization. Numbers were being converted to floats (1 became 1.0, 12 became 12.0, and so forth), so Adobe changed that by converting all numbers into strings (11 became "11", 17.24 became "17.24"). This was wrong too, as numbers weren't numeric anymore. At the time it raised quite a stir.
They fixed this (Bug 83638) really quickly, releasingCumulative Hotfix 1 for ColdFusion 9.01, which fixed the issue of integers being converted to float and having them as numeric values (ie: [1,12,true,"this var",17.24]). Hurray! Except....
Enter the improperly titled Cumulative Hotfix 2 for ColdFusion 9.01. I say this because it really isn't 'cumulative'. Most things are straight, from a cumulative standpoint, with the seeming exception of the fix to JSON formatting. If you have not applied CHF 1 prior to installing CHF 2, then you will still have issues with JSON formatting.
Overall, Hotfix 2 is great, fixing many bugs. The install is crazy/scary, and must be followed to the letter to prevent major issues, but it's worth it. As long as you did apply CHF 1 first, that is. Thankfully the hotfix/upgrade install process is much better in ColdFusion 10.
Big thanks to Ray for helping me to realize that I wasn't crazy, and pointing me in the right directions for all of this info. Hopefully this helps someone down the line.