Does he pull his legs up too? And is there much vomiting? Could be reflux - like the others have said. You can try raising up his cot mattress a bit and keeping him upright after feeds (maybe feed him when he wakes up, instead of before going to sleep during the day). My kids also hated dairy when i was breastfeeding. I'm not sure if you are b/f or ff, either way, you can try going off all dairy for a few days and see if that helps or try Goats' milk formula (which made a huge difference with my DS1).
ummm, otherwise, I'd say it sounds like wind b.c that's what my 17 week old DD does when I haven't got it all up. There's also a wonder week around the 12 week mark, and/or he could be starting to get teeth?
Has this behaviour just started? I remember a GP saying that if they get an ear infection, it hurts much more when they're lying down. Just another option? Hope you work out what's annoying him and get him sleeping better soon