Okay, I know a few of them! :)

The top picture: "Tall mountain thingy. I see a whole for something to go in, and then there's some sort of doorway at the top, but I have no clue what it does. And on the right another mountain tunnel/crane thing. I assume this works like a tunnel and I place it over the track, but does it have other parts that are supposed to go to it?"

That looks like it would go with an elevation set (comes with the pieces to lift the track up in the air) and have track that can go up to the house on top and run through the tunnel as well. Not 100% sure though (Boy, you have a lot of pieces we don't have and I thought we had most!) Crane thing, I think the one in the next picture that is orange goes with it, but not 100%.   Check this pic out http://www.fisher-price.com/UserInputFiles/photoupload/1cc802ab873749d3a0ed3c4ea418188d_400.jpg

"Little house, no clue if it does anything other tha look cute, but it does have some sort of crane thingy on the left of it.  And on the right some sort of house with a strange set of "docking station" looking things in the back. What the heck is this for?  I show the back in the next picture."

It mainly just looks cute. The crane came with more little tubes that it can lift off of one train car and onto another on an opposite track on the other side. No clue about the dock, maybe the roundhouse type building?

"And then there's some thing that you put something in the top, twist something and it rolls out the bottom into a train car (we figured that part out). But what the heck is supposed to go in it? I"

There should be red tubes that roll through that building and into/onto a train car. I believe that building came with a blue set of train cars that have one side that flips down on each car.

"Tunnel and bridge. I think the tunnel just stands alone and goes over the track, right? But the bridge confuses me, it doens't fit together and so I'm not sure what piece I'm supposed to be looking for to make it work?"

  Can you see in this pic the green tunnels/ramps? http://www.fisher-price.com/UserInputFiles/photoupload/a4345e90934649ef9826cdf8d9888b52_400.jpg, there is just a straight piece between them - not the suspension bridge, look right in front of that.

There should be a connecting piece or two for the green ramp/bridge. They don't connect to each other, but to another straight piece of track.

Well, with Geo Trax, anything basically goes with anything else, as long as they snap together!! :)  I'm sure you and all your boys will have tons of fun with them!

We have the fire station, gas station, airport (kinda cool), the water tower (which John LOVES because you can push down the spout-guess 1 year olds find that fascinating!), the coal chute one (the boulder/coal spirals downa ramp thing-I think I like that one more than the kids do!).  I like the Grand Central Station, but it's pricey and well, frankly we already have toys r us in our playroom so unless a LOT disappears once school starts, there will be no Grand Central. Edward is liking all the road signs right now since he's finally figuring out what they are for. He also LOVES the trains that go backwards and have people with them (we have Smokey and His Friends the fire truck one). 

I think what I love about Geo Trax is that it amuses ALL ages. Like John was 6 months old and LOVED to sit and watch the trains go, Edward could use them at 2 years old himself (John does it at 1 1/2 but can't put the pieces together that well just yet), my nephews who are 13 to 18 love to play with it when they come, my 31 year old husband and 66 year old father love it. It's not baby-ish at all, so everyone can do it!

The yellow thing is part of a pipe factory, I believe.  It's used to lift and load or unload pipes.  I have one but have never seen the pipes.  Might use some old AAA or AA sized batteries.

The tall green mountain in picture two goes with the single green thing in picture five.  That's called "Mile High Mountain".  You will need some specially curved green elevation ramps to go with them, plus maybe a couple of grey support pieces, especially if you add elevation track to it.  The little Alpine house on top of Mile High Mountain has a door that if you put one of the little plastic blocks (representing a crate of freight) into the door and then close the door, it falls through and comes out the bottom, where presumably one could have a truck backed up to the chute opening.

This guy might have some things you need or can give information:

http://geotraxworld.com/modules/newbb/report.php?forum=20&topic_id=350&post_id=1487

The two green bridge pieces go together but will need a piece to connect them.  Might need a special piece.  There are about 3 or 4 different bridges, at least two of which take special connector pieces.  Look for a grey, wide straight piece.

The thing that looks like a train station (in pictures 3 4 and 5) and has four empty slots in back is to hold four remote controllers, although some of the newer remotes, such as for Erol train (comes with Grand Central Station) and at least one other are too wide to go into the slots.  You can put batteries into that train station and it helps create train sounds.

The other thing in picture two is "Blaster Mountain".  Look that up on ebay to see the whole configuration for that.  If you email me (henrystinson@yahoo.com), I can send you pictures of my layout, showing blaster mountain and mile high mountain. 

The green elevation ramps and track you can buy on ebay and also the grey support pieces.  You can buy extra track and trains on ebay, too.  All you have to do is search for GeoTrax on ebay.  It can get very addictive -- and expensive, fast.

You might try buying a couple more big sets of GeoTrax stuff off craigslist and put together what you can and sell the rest.  Be patient when shopping on craigslist and look for big sets at cheap prices -- then act fast.