1) From an electrical perspective, you always connect negative of charger to negative of battery. The closer the better (i.e. put the clips directly on the battery) to avoid losses and heating in the wiring of the car. 

To check for this put your voltmeter across the battery when you are charging, then put it across the output of the charger. Any difference is lost in the wiring. A voltage under about 13.2V at the battery means either your battery is just about dead, or very little charging is taking place. Reading the amps going out the charger will also reveal much.

i.e. watts in = volts @ charger*amps at the charger
     watts into battery = volts@battery*amps @ battery

     difference = lost power == heat
     losses are either in the wiring, or are being used by some electrics in the car. 

2) Always do this in a well ventilated place, preferably away from the car and other flammables. Hydrogen, Oxygen and combustables (e.g. your house) are not your friend.

3) Observe basic safety precautions - open battery breathers (if present), fire extinguisher, circuit breakers, equipment fuses, gloves, eye protection etc.

4) Hydrogen build up is mainly due to electrolysis that takes place at the electrodes as part of the charging process. It doesn't happen when you are driving because the vibration loosens the hydrogen and oxygen bubbles from the plates all the time. In the static 'charging' situation this doesn't happen - so you can do it by lifting a corner of the battery about 10mm (1/2 inch) and dropping it about every 1/2 hour. You will hear the bubbles coming to the surface. If you are in a well ventilated area, all is well. If you are smoking you may singe your eyelashes.   

5) You are more likely to have a spark ignite hydrogen at the end of the charge process than at the beginning (see above). Switch the charger off at the wall and wait for everything to settle before removing the leads.  

6) Attaching the leads is more tricky since you will get a spark either way round - either the residual battery charge feeds the charger(if the charger is off), or the charger feeds the battery and sparks (the charger is on, battery voltage is low). Either is sufficient. There is no substitute for doing what you can to get rid of these naughty gasses - ventilation, vibration, time. 

A car I had in the 60's - I think it was an original mini or Beetle actually had positive battery terminal to chassis. Blindly connecting charger negative to chassis and positive to either pole of the battery would have caused problems (read fire, smoke, brokenness) in the charger, battery or car - especially in the old equipment we used back then. 

If the battery to chassis connection is poor, the car will not start anyway since much of its power will go into the bad connection rather than the starter motor. This place will get hot and burn you or the car or both.

We old timers chuckle at the safety precautions that are so often taken to ridiculous lengths - until someone loses a house, car and perhaps life.

Only then do we understand.