I've been having lots of problems with it lately, and I want to incorporate counters into my teams. I was thinking Cloyster, what else?
Heracross is the most dangerous threat to Sableye in the tier. It doesn't care about Taunt, and Will-O-Wisp and Toxic actually benefit it due to Guts, making Sableye easy to KO with a boosted Megahorn. Iron Ball and Lagging Tail will cause problems for it though. Victini and Darmanitan also fall into this category, as they are immune to Will-O-Wisp and will OHKO Sableye with V-create and Flare Blitz, respectively. However, they need to be careful switching if Sableye is carrying Foul Play, as it will OHKO both of them. Faster Prankster users, such as Tornadus, Whisicott, Murkrow, and Speed invested Sableye will toalways stop Sableye if they carry Taunt
Aside from what PB said, Magic Bounce stops Sableye in its tracks,most Sableyes don't carry an attacking move,and if they do,it's usually Night Shade,Espeon and Xatu can take Night Shades and Set up on it.