Thanks guys, for the advice.
This is actually not Honday warranty.  It's Penn Warranty, and was
given to me for free for a year by the dealer I bought the car from.
Does that make a difference in your opinion?

I picked the car up, and the ball joint problem is fixed.  He said he's
never had a warranty come through there that paid the taxes on a job.
Total price for the whole thing came to $550, which was less than the
700 I originally thought.  He lowered his labor rate so I wouldnt have
to pay the difference (his labor rate is normally higher than the
warranty's labor rate).  So in the end, I paid $80 for the allignment,
and $50 for taxes on the whole job.

Yes, I'm in the US - east coast.

I'm glad someone responded. I too thought something was
weird about having to pay taxes on a warranty item, for one
thing.

To the OP: If you're in the U.S., I think you should consult
American Honda's customer service about this, with tact, not
pointing fingers just yet, but to see if they too
immediately report what the dealer did sounds fishy and
deserves some scrutiny. There's a toll free number etc. at
http://automobiles.honda.com/

Something is wrong.  I recently had to have a steering rack replaced  under
warranty.  I dropped the car off and then picked it up later with no money
out of pocket.  It included all parts and labor, including an alignment.
You eigher have a truly crappy warranty or someone is lying to you.  
--------------
Alex

I wanted to post an update of where the car is at, and hear what you
thought.

The work on the upper and lower ball joints on the two front wheels is
being fixed (and luckily covered by warranty).  I was told by the
mechanic that after doing this, one must do the wheel alignment,
otherwise I would have steering problems.  Turns out the warranty never
covers wheel alignment, and does not cover taxes on the whole job.
Also turns out, mechanic told me that the WHOLE job, inc tax and labor
and alignment and all the upper and lower ball joints on the front 2
tires.... would have been $700.

What!?

I was shocked, considering I purshased the car mid-January, and now we
are in Mid-March.  That's actually just two months later.

So, please tell me: Is $700 for that whole job what could be expected?
He said its not something I would need again for another 90k miles.
Also, how much is wheel allignment on its own, usually?

The positive side to this, is I only have to pay $140 out of pocket,
for what warranty won't cover.  And I got a free rental car duing this
whole saga.

But still, if I didn't have that warranty..... $700???

What do you guys think?

No such thing as "Left Front Ball Bearing". Perhaps you mean "Left Front
WHEEL Bearing".

Squeaky lower ball joints are common.

What you're reading online is wrong. Squeaking can be a SEIZING balljoint.
Clunking has little to do with Honda balljoints. You CAN get clunking from
stabilizer bar link balljoints, such as those on many Toyotas.

Power steering boost will mask a seizing balljoint, and all you'll get is
the noise and no increased steering wheel effort.

Even a loose balljoint can be completely missed by most owners, as they'll
have got used to the vagueness of the steering. Keep in mind that a car
with rack-and-pinion steering and worn balljoints will track better than a
older car with perfect balljoints and a steering box.

Different from all of that. Coincidence. This is what warranties are for.
Guess that dealer's sorry he picked up this particular vehicle.

In January of this year I purchased a 2001 Honda Accord, 60k miles.
Before I bought it I had a mechanic look at the car, and he determined
that the "Front Left Ball Bearing" needed to be replaced, along with 2
tires.
So the dealer agreed to make the fixes before I drove it home.  They
replaced the Bearing, and put 2 new tires on the car.

Now its the end of March and all has been fine up to this point.
Saturday I started noticing that the car had a squeaking sound coming
from it as I drove.  It sounds like metal squeaking and was coming from
near the tire area.  It was especially noticable when going over bumps
or small hills.  Any sort of up-and-down impact driving, and the noise
would come back.

I brought the car back to the dealer (I'm under warranty, thank
goodness) and they put it up on the bay.  They said that the squeaking
sound is coming from bad Upper and Lower Ball Joints in the front and
it needs to be replaced.

My questions are:
--> Do you think this assessment is accurate giving the sounds I was
hearing?  Online I read people usually hear clunking sounds, and have
trouble steering.  I had none of that.  It drives great, just the
squeaking is getting louder and more consistant, on highways too.

--> Does it seem weird that the car was in fine shape when I bought it,
and just 2 months later the ball bearing is this bad?  They told me
this is standard maintenance type work on a car, and it's quite
possible no one could notice it back in January.

--> Do you think this is related at all to the Ball Joints I had
replaced, or the new tires?

Thanks!