Nine months is "supposed" to be the prime age for Separation Anxiety, but not all babies read the books and co-operate schedule-wise.
Josie went thru hers around 11 months, and she NEEEEEEEEDED to be with one of us a LOT while she went thru it! To top it off she was growing molars (hard for them to be distracted from pain when they're all alone in the dark) AND she had a stomach virus and puked for a day and a half straight at the time.
If your LO is working on molars, try some pain meds about 15-20 minutes before bed and see if it makes a difference. If so, you're on to something, even if the pain might also be from a latent ear infection. (If teething isn't suspected but pain meds help anyway, take to doctor, 'cause not all ear infections have obvious symptoms other than an out-of-sorts child - voice of experience here, even at 7 years!)
Have you recently started a new food? If he's got a tummyache that popped up in the middle of the night, that's no fun. Also, we found that as our girls began walking (and running!) more, they would get leg cramps in the middle of the night; snuggling would sometimes help distract them, as would being held just the "right" way, but otherwise they'd be miserale. (Took us AGES to work out the leg cramps too!) There are homeopathic meds for leg cramps; check at a health food store. Hyland's makes one that says not to give to kids under 12, but we've given them to both our girls (almost-4 and 7) for about a month now and relief has been pretty quick in coming, to the point where we've given them at bedtime to PREVENT them if they've been running/biking/doing karate/otherwise doing more leg work than usual.
Anyway, a couple thoughts that might be worth checking into.
