Well, obviously for ADR's, TS meals and such you tip (counter service, no lol), so depending on how often you eat at those places during your trip, I can't tell you how much tip to bring for THAT.
Now, as for the others, I'll knock em' off one by one. LOL
1: Magical Express - if you're not taking your luggage with you onto the ME bus, and having Disney deliver it for you, then you don't tip, because you won't even see them. If by some chance you're in your room when they deliver your luggage, I'd say $1-2 per bag would suffice. That depends on if you believe they should get a tip. This position is a tricky one, tip-wise. Now, if you're taking your luggage WITH you, and when you get to the resort, the driver comes out to take out your bags, then yes I say it's alright to tip. The same rate for this as well, $1-2 per bag.
2:Transportation to the parks - in most cases, you DON'T tip these CM's. They are simply doing their job and aren't going out of their way for something or someone specific. IF however they do go out of their way for you, whatever it may be (helping you with something, doing something out of the ordinary to make your experience 10x better, then I say you tip. Once again, same rates as those with the ME service.
3: Mousekeeping - the majority of people tip these CM's, either out of sympathy for what their job entails or just appreciative of cleaning their room. Usually it's a $1 or so per day, unless they do something special, like make a towel animal, place one of your stuffed animals (if you have kids) on the bed and make it look like it's watching TV with the remote, etc. I highly suggest tipping every day, as apposed to all of it at the end of your trip, mainly because on your last day, you could very well have a different Mousekeeper clean your room. If this happens, you'll be leaving the tip for someone else to that new person, who hasn't even touched your room yet. This wouldn't be fair to the Mousekeeper that cleaned your room all week and made your trip just a little more magical.
I say leave a note with your tip if you want. It doesn't have to say anything lengthy. Just a simple "Thank you!" would suffice. I'm sure that keeps the Mousekeeper's spirits just a teensy bit lighter during the day. I know it would for me!
In the end, go with what YOU think. If you think a certain someone should be tipped based on what they've done, then give them a tip. No one's stopping you. The CM's will surely appreciate it!