Your title says Catapult, but your post says Cannon...
Either way the answer is cannon
Seriously though: They really all have useful places, some just more than the others.
Doomwheel: Monster hunter extraordinaire. With the relative lack of monsters seeing play though, the Doomwheel generally gets relegated to flanking on block units to try to break them via
CR (when combined with a frontal charge of course!) Sadly, as much as I love the model he's the least useful of the Skaven rare slots.
Plagueclaw Catapult: Large pie plate of no-armor-save doom! Unfortunately, it hits at S2 which means actually wounding can be a bit of trouble. Now, a couple applications of
Wither from Lore of Plague will make it easier to wound for sure, but it still means the PCC doesn't stand as well on its own.
Hellpit Abomination: Commonly considered absurdly overpowered/underpriced, I've yet to see massive return from mine. A common remark is that he's really, really hit or miss. He tends to either do extremely well at wrecking your opponent's face in, or he tends to run into a flamey burning death. That said, the look on an opponent's face when he gets back up after "death" is priceless. Get's second place in rare slots.
Warp Lightning Cannon: I will be the first to admit that the WLC could probably use a price hike. For a paltry 90 points you get one of the best, all around units in the game. Good at monster killing due to (potentially) high S shots, no armor saves and multiple wounds (
d6). Good at unit killing thanks to the small template explosion at the end of the "bounce". Good at killing mobs of multi-wound models for both the above reasons combined. The WLC is my go to killing machine.
People complain about double HPA, and with how hard to kill the thing is I can understand it. But if my choice came down to two HPAs and one WLC or 2 WLCs and 1 HPA, I'd take the two WLCs every single time.
Plus, come on... it's a cannon that shoots LIGHTNING!