If it's more noticeable in 1st, less so in 2nd (sometimes have to be in a quiet area, and get the revs up) and can't make it out at all in 3rd-5th, I thought that could also be the mainshaft bearing. I don't really know, but I've read that.
(edit: Just so we're clear, I'm talking when you leave it in gear and have the car rolling but the clutch is disengaged, to the floor. Getting the revs up in said gear, then only when you put the clutch in can you hear it. If you are hearing a bearing noise from the trans. over the sound of the engine while driving, with clutch engaged, that would be a much louder noise and more serious issue.)

Mine's the same way ('92 EX) for what it's worth, been like that since I got it and doesn't seem to have gotten any worse.

If you have it at idle, in neutral, and you let the clutch pedal up, do you hear a noise as soon as you start to engage the clutch? If so, I believe that's the mainshaft bearing you are hearing. Most used cars w/ manuals I've been in make that noise (most of which have been Hondas), at least when I've bothered to check for it.

I can't say for sure the sound at idle w/ clutch engaged is the same thing causing the noise in 1st, but possibly.