1) He came in
the bedroom where I was and just stood there.
2) He came into
the bedroom, where I was and just stood there.
I say it's (2), or does it matter?
Sorry for the delay--I've been on vacation, and was in airports most of today.
It definitely matters, and you're right--it's #2 (without the comma).
Here are are few more sentences to illustrate the difference:
She tossed a ball in the lake.
This sentence says that she was in the lake--and that while she was there, she tossed the ball.
She tossed a ball into the lake.
This sentence says that she was on the shore (or somewhere else NOT the lake--perhaps in a hang glider above it) and she tossed the ball so that it went into the waters of the lake.
A few similar sentences with a related pair of words:
Jan hopped on the chair.
Jan hopped onto the chair.
In the first sentence, Jan was already on the chair and she started to hop. In the second one, Jan was on the floor, and after hopping, she was on the chair.
I'll leave it to you to determine the two possible meanings of your original sentences.