I remember when I first started battling on Battle Tower Wifi some that stood out were (and my grumbling predjudices haven't changed):
Weavile: Bastard outspeeds so much (and can ice shard to outspeed the rest). Its 3 attack types have ridiculous coverage, and with pursuit and ice shard for variation it's still hard to predict attacking. With Taunt, Counter-Sash, scarf and band variations also running around, it can be a major pita to take down without losing a valuable poke.
Porygon Z: When a special attacker can potentially 2 hko blissey, (or even 1hko with hyper beam) you know something is just plain wrong. Able to speed or special attack boost with download or just extra stab its tri-attack with adaptability, and also make ridiculous good use of specs, scarf or nasty plot . . . sickening, just sickening.
Togekiss: Scarf version ruins teams in the tower. Parahax is a bitch on wifi. This thing is the cheapest shit this side of wobbuffet.
edit: also 2nd the comments on breloom and Yanmega.
thought about it more and added:
Hippowdon: How do you take this thing down without it being such a PITA?? There's like NOTHING that can really stop this thing from doing its job as a lead, seeing as it laughs at pursuits and just needs to COME IN to set up sandstream, which is completely game-altering.