Because code is updated daily, a change meant to fix one system can occasionally break something else. If a new update causes crashes, you can easily download an older Nightly build from the archive until a patch is issued.
While superior, Nightly builds are not without risks: pcsx2 nightly
Historically, PS2 emulation relied on separate plugins for graphics, sound, and controllers (GSdx, SPU2-X, LilyPad). In Nightly builds: Because code is updated daily, a change meant