1999 Civic DX Sedan 5speed/manual.
Stock motor, stock suspension, 17" Konigs Heliums on low-profile tires.

(I can't lift up the car, my jack and stands are with a friend)
This sound is new, I started noticing it within the past few days. Double checked the tires PSI and brought it back to 34~36, also checked the lugs to make sure they weren't loose.

At first I thought it was the shift linkage but it sounded like the noise is towards the wheel and not the linkage (i took off the linkage a month ago to install an integra dual-bend shifter). I also thought it was the clutch fork because the noise happened when I shifted from 2nd-to-3rd and it sounded like it came from that area (i have a squeaky clutch, and grease now and then using this DIY). Then, I went out for a drive and when I took off from a stop sign in 1st gear slowly, I started hearing a metal whining/clunking sound and so did pedestrians notice... After that whining/grinding on my way home going up a hill my car started to shake unusually at 35mph.

Any ideas?

 

Sounds like a wheel hub bearing. When you get your jack back, jack up the car, and grab at 12/6. Try to wiggle it. Grab again at 3/9, and try to wiggle it. If it wiggles both directions, that's a pretty definitive wheel hub bearing diagnosis.

 

Yeah I would've done that if I had the jacks, one of the basic things my instructor taught me in automotive. Why would it happen when I shift from 2nd to 3rd though? When I shift smoothly, it pops, but when i'm sort of gunning it and sped shifted it didn't pop/click.

 

Driveline shock? I honestly couldn't tell you, it just sounds like classic bearing noise to me.

 

Hmm I really need to get under there and check my explanation is too vague still, thanks for mentioning a possibility. It actually could be the wheel bearing my Odyssey's was bad too and it does feel like a wheel bearing again.

 

check the outer tie rod bushing. don't need to jack the car up for that. it could be missing