Yes, you are free you use custom server JARs, including, but not limited to:
- CraftBukkit (including unstable beta and development versions)
- Spigot
- Forge, including Tekkit, Feed The Beast, Pixelmon, etc
- BungeeCord (as both a hub, or servers in a BungeeCord network)
Does HostHorde support non-vanilla servers?
Information regarding what types of servers HostHorde supports.