When wrenching on the battery, it's generally a *REALLY* good idea to
pull the negative clamp before doing anything on the positive side -
When the negative side is hooked up, any contact between the positive
post and the body of the car equals "dead short" - The level of
"interesting" that results from creating such a short can vary from
"look at all the pretty sparks" to "Wow... I didn't know a wrench could
be turned into a puddle of glowing hot liquid so quickly. Boy, it really
sucks having a wrench turn to liquid and dribble through your
fingers..." or a near infinite number of variations between those
extremes. So yes, it's a good idea to disconnect the negative side
before you put a wrench n the positive side. Since the negative post is
already connected to the rest of the car, it doesn't matter if you bang
the wrench against the body while tightening (or loosening) the bolt on
that side.

As far as the "negative side controls the rest of the car" - I don't
recall seeing that post, but if that's what got said, whoever wrote it
was talking out his a.s about something he clearly knows *ABSOLUTELY
NOTHING* about.

As for the rest of your trouble, like others have said, get that clamp
tight. And don't be horribly surprised if the alternator is toast - As
stated elsewhere, the alternator can do some really odd things when the
load presented by the battery isn't in the circuit like it should be. As
an example, I had a cable shake loose on a washboard road one night
while doing my paper route. Within a matter of seconds, I lost every
light bulb that was powered up at the time - Both headlights and all of
the marker lights fried, the dome light popped, the bulb in the radio
puked, and I had to replace every one of the "light up the instrument
panel" bulbs. Fortunately, the vehicle was an older rig with no computer
to be fried by the massive over-voltage, so I was able to drive it home
once daylight came and I could see to drive, but I have little doubt
that if it had a computer module in it, that would probably have cooked
off and outright killed the vehicle.

Not if you attached the jumper battery to the clamps directly.  If it
still doesn't start, or at least try to (the jumper battery may not be
quite strong enough to start the car all by itself) you may have more
issues than just the clamp.

nate

Well, I just spent a whole day with the car.   First I tried to use my jumper
battery and after that didn't work, I went for a gallon of gas, thinking the
tank was near empty.   That was also no help, so it was time to call for a
tow to the repair station.    Once I got it in for repair, the first
diagnosis was the distributor went because there wasn't a spark when trying
to start the car.  Remember that there wasn't a problem with the battery as
the lights, radio, and engine were cranking.   The engine just wouldn't start.

After I came home, I received a call from the tech who said that upon further
inspection, it wasn't the distributor.  When he looked under the dashboard,
he noticed my computer was missing!  
That's probably why I saw the positive battery clamp off the terminal last
night.  When someone broke in to steal the computer, to shut the alarm they
disengaged the positive clamp from the battery.
Why would anyone want a 1995 Civic Ex computer?   Is this common?

I don't know how a thief into the car so easily.   There's a Chapman lock for
the hood, and there's no sign of forced entry.  

Anyone know where to get a new one?   I see that RockAuto has one that has to
be ordered.

yep

the honda clamps are crummy
aftermarket clamps attaching to the cable are kind of klugy, best to
just get a whole cable with clamp.
note that the honda positive clamp has another terminal where the
wiring for everything except the starter attaches. make sure the
replacement cable has this.
which brings me to the point: make sure that that connection is still
connected on your current loose clamp; if they left the clamp loose,
they may well have left that disconnected. although i think that would
probably not let the starter spin, but who knows....