Technically, pitches aren't tools, but it's easy to lump them in with the other tools when discussing the 'bests' in a system.
There could be some debate as to whether the best fastball is the fastest, or the one with the most movement. Since even 100-mph pitches will be killed if they're flat, movement is probably the more important of the two, and there may not be anyone on the farm who gets more movement on his fastball than Chi-Chi Gonzalez. Normally sitting around 90-94, Gonzalez hit 95 a few times and 97 once in his last start with the RoughRiders. While his command and control are still developing, Gonzalez has the pitches to be an extremely solid major league pitcher. Luke Jackson's ability to consistently hit 97 as a starter puts his fastball in a similar position, along with the plane he gets on the pitch.
Pure velocity-wise, Keone Kela's fastball has returned to where it was in Spokane and the Arizona Fall League last year. Regularly sitting 98, and touching 100 in his home appearance on August 9th, Kela has the hardest fastball in the system, and this year it's not only been fast, but he's added some life to it as well, running it in on the hands of right-handed batters. Though his curveball isn't at the level of others mentioned later, he's figured out how best to throw it, and in his last few appearances, he's looked better than the competition. (Edit: According to the stadium gun in Springfield, Kela hit 100 and 101 on back-to-back pitches on August 12th).
Alex Claudio's changeup isn't just the best in the system, it's one of the best pitches to view live. The screwball-esque pitch usually comes in anywhere from 64 to 69 mph, and the visual of hitters flailing over it tells you almost everything you need to know about it. Lisalverto Bonilla and Edwar Cabrera, both in Triple-A Round Rock with Claudio, have fantastic changeups of their own right, and Cabrera's change allowed him to have success as a starter in Double A this season (2.99 ERA in 17 starts) before his promotion to Round Rock.
System newcomer Jake Thompson's slider impressed immediately, and is probably one of the best overall pitches in the system. Thrown in the low-to-mid 80s, the pitch has an almost ridiculous amount of horizontal break, and he can throw it for both called strikes and whiffs. Impressively, Thompson doesn't use the pitch as a crutch, keeping it to use as a true weapon rather than relying on it if his other pitches aren't working as well. Round Rock reliever Jon Edwards also has a solid slider, one described as being of 'big league' quality, which he pairs with a high-velocity fastball.
There are some nice looking curveballs in the system, including Luke Jackson's and Corey Knebel's, but if pressed to pick a single pitch, Myrtle Beach closer Jose Leclerc's 73-77 mph breaker takes the title. When he throws the curve well, it comes in with big movement, usually staying on an 11-5 trajectory from his very high three-quarters arm slot. It comes from the same slot and with the same arm motion as his 93-96 mph fastball, making a pitch with good break even more effective. Knebel's takes a similar motion, in what video footage is online, but has a slightly less-deep shape, while Jackson's is an extremely solid secondary pitch, but has less velocity separation than Leclerc's.
Finally, command, here generally defined as 'the ability to execute a plan of pitching attack,' throwing one's pitches with accuracy. A great deal of the time, pitchers with this ability also demonstrate clean and efficient mechanics, such as Alec Asher and Jose Monegro. Despite some rough starts recently, Asher's command is still among the most impressive in the farm. His walks against strikeouts reflect this, as he historically and currently has shown the ability to limit free passes, while getting a large percentage of his outs via strikeout. Organizational warrior Jose Monegro also has this ability, hitting his target a great deal of the time, with the added bonus of doing that at almost every level in the Rangers system. While both Monegro and Asher rely on strikeouts looking, Alex Claudio demonstrates his ability through setting up the changeup to induce that swinging third strike, while also not walking many batters.