A well-designed amplifier or powered speakers will not pop when powered off. Internal safeguards will mute the power amp a few milliseconds prior to shutdown. You're doing it right by shutting down everything in reverse order of the signal chain.
 
As to whether such pops can damage speakers, the answer is yes - but usually only at very high power. Damage is not likely for hi-fi systems or active studio monitors. Just don't try it at a 50,000-watt concert venue.

I own some earlier SWR bass gear (pre-Fender), Bass-350, Bass-750, Super-Redhead, and WorkingManSeries-700. The latter has what bitflipper suggests, where it will Mute the signal prior to releasing the pops. Conversely, and SWR claims this is to remove circuitry to purify the signal better, on the Bass-750,350 or Super Redhead, these would pop sometimes when powering up or down since they never employed that type of circuit. But they do recommend disconnecting the speaker cable before turning the amp on. This could be a situation similar to yours where the signal is somehow still active after power has been disconnected. 
 
To equal bitflipper here, my Pass-350 mastering amp has some protection built in to is so that it will not destroy speakers, because it otherwise surely could (and has before) blown tweeters in my older mains from some dynamic material at high volume. I recommend powering down your mains amp before the sub, then the sub, then everything else.

The nice thing about a great amp is that will only fry speakers that truly aren't able to handle it's power output.
 
If you're lucky the amp will have protection for the amp should you fry a speaker and end up with a short instead of an open.
 
Frying tweeters is a right of passage. You can use the opportunity to learn how to use a crossover, either passive or active with a bi-amp strategy. I would imagine that most folks who have been there have done that. I think that I've fried more stuff with under powered amps than I have with the good stuff.
 
best regards,
mike

I have a Sub and two monitors and a separate crossover hooked to a Monster Power Pro 3500. When i power on the system the crossover comes on first and then all speakers come on a few seconds later. It powers down in reverse. There is no noise or pops what so ever. I dont like pops in anything, Guitar rig, audio system in my truck etc. So i totally understand the question!

Any noises or pops you may be hearing after you have turned your power amp off are almost certainly due the the residual energy that has been stored in the electrolytic capacitors in the power supply. Although this energy may be still there for a little while, it should not be causing your speakers any harm as such. It usually dissipates fast because the capacitors are not being recharged.
 
What are the woofers doing when these pops occur? If they are not moving at all or very much then you really don't have anything to worry about. Any talk about frying speakers more than likely won't be an issue here.
 
It is things that can cause serious turn on thumps you have to be careful of. I had an older Kurzweil K2000 rack synth that sent out the most horrific of signals on turn on. Enough to move an active monitor woofer about 3 inches! (I don't have it now and the new Kurzweils are perfectly silent on switch on now)
 
A good rule of thumb is when turning on any gear connected to your system anywhere keep your monitor levels off/down or mute the mixer channels while you do it.
 
And Dave I have done something similar to a 50.000W PA live in front of a big audience and it was not pretty! (but don't we all have to have that happen at least once to us in our lives!)