The 9VAC available at the Commodore 64 User Port was used to drive additional peripheral loads that were not convenient to drive from the +5 VDC supply, or when doing so might exceed the limited current capacity for the DC supply. Both supplies were rated for 100 mA, so you could carry significantly more load by utilizing both supplies. Such uses also existed internal to the C64, where the system's 9 VAC was used to derive the voltages for the SID (~12V) and for the cassette motor (~ 6V).
An excellent example of this is the VIC-1011 RS-232 adapter, which uses the User Port 9 VAC in the generation of the 12V signals needed for RS-232. A schematic for the VIC-1011 shows this.
Common peripherals for the User Port, besides RS-232, were modems, printer interfaces, and EPROM programmers. A number of retro modems are designed to utilize 9 VAC, but I don't have a specific reference showing a modem for the C64 that used it. This EPROM programmer schematic does use it.
With flexibility as a goal, Commodore may have also meant for the 9 VAC supply to be useful for small motors, or to serve as a stable frequency input, as was also done with 9 VAC internally driving the TOD clock.