If there's a regular spot where he goes, maybe try putting a box on that exact spot. We had a similar problem a few months ago, where our cat was peeing in the basement on a stack of paper he found. We moved everything away from that spot and put a box there and now he's happy as a clam.
I ran into the same thing: Cat pooped in exotic, awkward places, but never the litter box. Never looked like she was in pain -- just being stubborn, I figured. Turned out to be a bladder stone brought on by the ingredients in modern cat food (put in place to help other feline health issues, but which causes stones in a small subset of cats). After the stones were cleared up, all litter box issues disappeared.
My cats don't like the uber-expensive clot-forming synthetic crystal litter, and don't like various types of alternatives either - almost none from this list: http://www.petco.com/Shop/ShoppingGuides/petco_ChooseCatLitt... )
..but they do love some simple pebbles, which are, fortunately, dirt-cheap (or pebble-cheap :) ) although a little messier to clean than the above alternatives. I think they'd like sand as well (I live in Uruguay and those pebbles are from Argentina, so I don't know what alternatives are in the U.S.).
So in the utility room I used for the litter boxes, I replaced the carpet with some cheap engineered wood flooring (Pergo or some similar knockoff brand). Problem went away. I think it is very weird/uncomfortable for them to go on a smooth hard surface, and carpet is a rougher surface that sort of could feel like dirt or grass.
For two cats, we have three litter boxes that are cleaned daily, new litter is added every couple of weeks as the level of the litter goes down, and then the boxes are fully emptied and fresh litter added about every three months, and that keeps them mostly happy. Unfortunately, one of the cats will periodically pee outside the box even when the box is perfectly clean, and the reasons are many, and somewhat ambiguous.
Sometimes it's the litter. Either we're trying a new litter, or the manufacturer changes the litter, and the cat doesn't like the new litter for some reason.
Sometimes it's the environment. She's using the litter box and there's a sudden noise for some reason, and then she won't use that box again for a while. Not really a problem when we have three boxes, unless she's been startled while using all of them within a short period of time.
Sometimes she's feeling stressed out. If we rearrange the furniture, the seasons are changing (generally only going into winter does this seem to be a problem,) can't pay as much attention to her for a prolonged period of time, go on vacation, or bring home a new child, she's far more prone to peeing outside the litter box.
She never poops outside the litter box, only ever pees.
We've pretty much just formed a routine to minimize the peeing issues. We keep the litter boxes clean, we make sure we pay enough attention to her, and we try to encourage her to use her litter box at least once a day. If we haven't seen her pee in the litter box for a few days (does not mean she hasn't used it, just hasn't used it in front of us) we start to minimize the available options for her to pee in/on (easier than it sounds, she tries to find substitutes for her litter box, so anything box like, or that she can use to bury, like throw rugs.)
Great suggestion.
Cats do occasionally get run over, but most learn to avoid dogs and if they're getting second helpings of dinner at someone else's house, so what?
But it's the complete opposite in the U.S, and although that makes sense in some places (a lot more predators in the countryside), in a city like San Francisco the risks seem identical to those of London. It's very strange. Of course, in the UK cat owners aren't legally liable for their cat's actions (cats, unlike dogs, are deemed by the law to be free agents), maybe that's not the case in the states.
Cats do kill wildlife, but their impact is often overstated. The RSPB (Royal Society for the Protection of Birds) in the UK has no issues with cats being let out, but recommend they have bells on their collars. The majority of birds that cats kill are sick, frail, or otherwise in poor health.
To quote the RSPB: "there is no scientific evidence that predation by cats in gardens is having any impact on bird populations UK-wide"[1].
[1]:http://www.rspb.org.uk/makeahomeforwildlife/advice/gardening...
(We've had a lot of "missing cat" signs on the group mailboxes lately. Woods nearby. Expanding populations of fishers, coyotes, wolves, etc. Did I mention I'm 15 minutes from Parliament Hill? Bears downtown, -35 C winters (with serious wind and a whole lotta snow), +35 C summers (with 90+% humidity), wild beasties in the woods.... I really love Ottawa. I mean, I must. No rationale person would live here otherwise.)
On a serious note: cats usually integrate well with their ecosystem and if they would really pose such a big threat, smaller mammals and brids would just migrate away. edit: I'm speaking of balanced ecosystems where cats have natural enemies, foxes and whatnot.
That's exactly what you don't want happening in an ecosystem.
The majority of birds that cats kill are frail, in poor health, or otherwise likely to have not made it through the season anyway.
[1]:http://www.rspb.org.uk/makeahomeforwildlife/advice/gardening...
I doubt that those are all frail and doomed to an early death.
I've also seen way too many FIV+ cats come through the shelter system, transferred when they're attacked by FIV+ strays. If you ever need to give up your pet, FIV+ status is an immediate death sentence in many shelters. In no-kill shelters, it means a longer stay because some people are weirded out about "cat AIDS".
[1] http://planetbratfink.blogspot.com/2013/11/the-story-of-ange...