It's typical of Game Freak to create a wicked new ability in Prankster, which gives all support moves +1 priority, and then create exactly one Pokemon with all the gadgetry necessary to abuse every facet of it. Whimsicott is that Pokemon. Filled to the brim with nearly every support move you could possibly want bar entry hazards, Whimsicott is a supremely effective momentum grabber, stat-booster check, and general annoyance to anything on the receiving end of its boundless movepool.
Whimsicott, while amazing in its ability to support its team, is a victim of circumstance and nothing more. While it is very cool that it can check pretty much any setup sweeper, Whimsicott requires nigh-perfect prediction for it to be worth its weight on your team. Whimsicott's bulky, don't get me wrong, but you don't want to switch Whimsicott in accidentally on an attack that even 3HKOes it, because Whimsicott won't be able to set up properly and will either get beaten soundly or forced back out to another Pokemon. In this sense, Whimsicott doesn't really check Pokemon like other, more popular Pokemon can, and this is really the reason for Whimsicott's lack of usage. You can't—or rather, won't—switch Whimsicott into even Grass-weak Pokemon to threaten them out, as that's just not how Whimsicott works. You'll be relying on Encore, Taunt, Substitute, and other tricks to screw them up and force them out so Whimsicott can do its job. If you aren't planning on doing that, then stop right now and pick a different Grass-type Pokemon, such as Virizion or Ferrothorn. Don't let me turn you off to using Whimsicott totally, though; it's a seriously solid Pokemon if you can play to its incredibly specific strengths and predict like a beast capable of winning the Smogon Tour. All I've got to say is: "You've been warned."
I know what you're thinking: "This set has very few options in it, where are the rest?" Keep your pants on, because while Whimsicott has literally dozens of tricks it can play, what you see before you is the most reliable and best combination possible. If you want to adjust it to your tastes, be my guest, but this here is what the pros are packing.
Encore is perhaps the single greatest move available to Whimsicott. You can switch Whimsicott into any stat-boosting or otherwise non-threatening move, Encore it, and then completely go to town. Encore also doubles as insurance against anything that tries to set up on Whimsicott. Nothing will attempt a Dragon Dance, Swords Dance, Nasty Plot, Substitute, or whatever against Whimsicott thanks to the threat of Encore. Whimsicott's next best bet at annoying opponents is with its priority Leech Seed, which screws up and wears down anything that isn't Grass-type. After that, Substitute and U-turn are both good options. Substitute allows Whimsicott to wither down many opposing Pokemon as they fumble to break Substitutes and force Whimsicott out. U-turn is a better option for offensive teams that want to bounce out and use Leech Seed healing and an offensive threat to force switches and sweep. Stun Spore in the last slot is spectacular at paralyzing and stunting the sweeps of everything from Landorus to Venusaur. Meanwhile, Taunt can be useful at keeping something like Ferrothorn from coming in and throwing up layers of Spikes as Whimsicott looks on helplessly. Like I said before, these are just the most reliable choices for moves, you can mix and match pretty much anything in Whimsicott's movepool to create a cool and personalized variant of this fluff ball.Team Options & Additional Comments >>>
I had originally prepared an amazing paragraph for you to read, but rather than shoving a couple hundred words down your throat, I will instead just list the myriad of support moves that Whimsicott is able to abuse successfully: Cotton Spore, Cotton Guard, Tailwind, Charm, GrassWhistle, Memento, Switcheroo, Toxic, Sunny Day, Rain Dance, Light Screen, and Trick Room. Each of these has niche value on Whimsicott for specific teams, so you should amuse yourself and experiment with them to find the best combination for what you want to achieve. As an aside, you might sometimes desperately want an attacking move on Whimsicott for whatever reason. If you must, Giga Drain is the way to go, although Hidden Power Fire isn't bad for opposing Grass-types. Just remember that Whimsicott is pitifully weak offensively, and even more so if you're not investing any EVs in its Special Attack.
Checks and Counters
Do yourself a favor and don't switch in something in an attempt to use Whimsicott as setup fodder. That only works if Whimsicott both lacks Taunt and you're setting up entry hazards or ordering your own Pokemon to use Taunt. Speaking of Taunt, it's the best way to guarantee that you can force Whimsicott out. Tornadus happens to be faster than 0 Speed Whimsicott and has Prankster itself to Taunt before Whimsicott can do anything. Since Whimsicott almost never runs an attacking move, this either makes it kill itself with Struggle or gives Tornadus a free turn to attack.
Outside of the obvious Taunt, the best way to get by Whimsicott is to just hit it until it dies. Even Pokemon that normally don't like Grass-types, such as bulky Water-type Pokemon, can give Whimsicott trouble just by spamming Ice Beam. Most of these Pokemon won't like suffering the withering effects of Leech Seed, but a few can get around it. For instance, Whimsicott will only hurt itself if it tries to Leech Seed against Tentacruel, while Tentacruel can either smash it with STAB Sludge Bomb or set up Toxic Spikes if Whimsicott isn't running Taunt. Rain Dish Ludicolo can be a real pain for Whimsicott in the rain, as it doesn't take rain-boosted Scalds or super effective Ice Beams well at all. Using a Grass-type of your own is also a surefire way to put a damper on Whimsicott's shenanigans. Virizion can come in and use Hidden Power Ice to force Whimsicott out, while Ferrothorn can come in and either attempt to set up Spikes or do serious damage with Gyro Ball. Other less common Grass-types, such as Celebi, Shaymin, and Breloom, work as well if they just outright attack Whimsicott, but won't appreciate a U-turn to a typical check like Tornadus. Either way, just remember that Whimsicott is not an offensive threat in any manner, and if you're carrying any of the aforementioned checks, you'll probably fare just fine against it.