There is no other option besides smite for jungle Fiddle and for any jungler for that matter. You must have smite so you can control buffs/dragon/baron. Smite is one of the most important summoner spells in the entire game because it doesn't just help you, but potentially your entire team if you can secure a dragon/baron for global gold and experience.
With the recent overhaul, Smite can be used on enemies. It's best to get Stalker's Blade - Magus on Fiddle because Smite then applies a temporary slow. Smite's range is much farther than Fear, so smite for a slow and get into range to fear.
Flash is a must have on Fiddlesticks. You can cover a large gap with the Crowstorm + flash combo. Even a simple flash + fear can change a game in your favor. This spell has its offensive and defensive uses but generally you'll be using flash to get into the middle of 5 people in a team fight.
The runes listed above are a well rounded set of runes that enable an easier early game while providing the necessary scaling to help out your late game as well.
x3 Flat AP quints are an absolute must for your early game. It's a common misconception that Fiddle has a slow clear time in the jungle, having at least 20+ AP makes him very fast.
x9 Magic Penetration is pretty standard for any AP champion. These combined with Haunting Guise/Sorcerer Shoes later on will bypass a lot of the enemies magic resist. These won't necessarily help you in the jungle but they are a huge asset when it's time to team fight.
x9 Flat Armor runes are personally what I prefer to use in the jungle to reduce damage taken early on from monsters and slightly help if you get invaded by an enemy jungler.
x9 Health Per Level are also a good choice. Fiddle has low base HP and his late game health is also quite low so these can make you a bit more beefy late game. I often opt to go with health seals because I am good at avoiding invasions and the extra health better suits me for late game.
x9 AP Per Level are what I prefer to use. These will help you scale into the late game and you can get CDR from Blue buff/Athenes later in the game so CDR glyphs are not my preference.
x9 CDR Per Level/Flat (doesn't matter) are also a good choice. Fiddles ult has a moderately high CD unless you get CDR in your build, which is pretty hard. Since items won't give you much CDR in a standard Fiddle build you'll be getting most CDR from Blue buff or glyphs.
Fiddle is strongest in the jungle with an offense based tree but it is still a great idea to dip your remaining 9 points into the utility or defense trees because both have good masteries to offer early on.
Offense: 21/0/9 (My Personal Choice)
Offense/Utility is my first choice regarding masteries. Movespeed, summoner spell CDR. trinket cast range, buff duration, and improved recall are all very strong masteries to have from the Utility tree.
Butcher/Feast is irrelevant on Fiddlesticks because Drain does not get the bonus damage to creeps since it is a damage over time spell. Keep the same Offense tree listed above but put the remaining 9 points into Defense masteries like Tough Skin, Bladed Armor, and Juggernaut etc.