IPS is the most widely-supported, but 1. it doesn't work on files larger than 16MB and 2. for this reason, we're trying to break the community's overreliance on it.
Breath of Fire 2 should've been UPS, dammit. Don't know what I was thinking releasing it as an IPS.
For games which use a virtual file system, or in which you've had to move a lot of stuff around, an xdelta patch is probably the best way to go. Fortunately, KaioShin's developed a glorious
GUI frontend, which you can get here.