having started a new job last year, and been commuting ever since with SPD's, i would offer the same advice i was given when i first started cycling again after a period of 30 odd years out of the saddle, and this is:
If you are seriously considering a clip in system (Either Road (3 bolt clip in's) or off road (MTB) SPD's (2 bolt sole inserts) first ask yourself if you will be waring the same shoes when you get to work, or changing footware. it may sound like an odd question to start with, but if you ware the same shoes, this cuts down on the ammount of weight you carry on your back whilst commuting. If this is the case go for SPD's, the clips are resessed into the sole, and you can walk in them anywhere and they are extreemly comfortable.
Something else to consider is, if you get a puncture and end up walking home, road shoes are totally unsuitable for walking in, as the cleat is mounted on the sole of the shoe!
The advise i was given, put your bike in the kitchen and for a period of around 10/15mins, just prictice clipping in/out. this will help on your first outing and possibly avoid craching to the ground having come to a stop and forgot to put your foot down!