I am building a pauldarium setup in my 80 gallon tank. I am planning on having about 12 inch deep water with chunks of wood sticking out. I also am builiding a slate platfrom that willl come out from the back wall which i will rest plants, branches, etc. on. My question is would I be able to put pygs in there given they had plenty of climbing branches and vines without worrying about them getting in the water?

It sounds like an awesome set up. Probably not a good idea for pygs though. These guys live in damp mountainous areas, as opposed to lowland bogs or pond terrain. Do some more research, but from what I've heard, by putting them in a water environment you could risk death by drowning.

Not a good environment for them. If you want to keep pygmies you need to create a habitat that is as close to the natural forest floor as possible.
Additionally, if you are building an environment like this, I would assume it is for some other type of animal ... housing pygmies with any animal other than the same species of pygmy is a really bad idea.
Keep it pure (one species per environment) and create enclosures that are appropriate for the species you will be keeping.
-Brad

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I was also going to have mudskippers in the water. So even if I had a platform with a substrate and leaves on it the setup would be risky to say the least?

To say the least.
Mud skippers (very cool animals by the way) in their own enclosure and pygmy leaf chameleons in theirs.
These animals would not naturally live in the same environment.

-Brad

I hate to start a debate or be annoying but the mudskippers would keep to there water, sand bank, and driftwood while the chameleons kept to the branches. I just hoped that they would benefit from the humidity. I fully understand different species requirements but they are kind of seperate habitats within the same tank. I am BY NO MEANS and expert at all. I just want to create an interesting ecosystem. Thanks for all the help also.

No debate ... I will say, however, that an important element in pygmy husbandry is allowing the enclosure to completely dry out between mistings.
Will you be able to achieve this?

-Brad

If there were lots of escape routes out of the water, they can swim for very short distances. They puff their body up with air to stay afloat (however, if they don't get a chance to do this in mid-air, they'll sink like a rock).

It definitely would be risky.

I would recommend some dart frogs, or day geckos, or both!

Of course, this really depends on how much floor space you have, what species you get, etc.

As for pygmies, I'd say that ultimately it is a bad idea for that large of a water area.

The drying out between mistings is a good point. When I recently kept cichlids in the tank I would usually leave the canopy open at night to keep the moisture levels inside from going crazy and growing funky stuff. I dont know if that would allow enough drying though. I was also considering dart frogs.

I got the same lecture for having different species of frogs int he same cage.. I have 2 cricket frogs from a creek and a red eye tree frog..they have co existed for about 9 months together now and are doing great.. But because they wouldnt "normally" exist, I was told this is unacceptable. I say if they have SIMILAR systems and you are able to maintain temps, humidity, and as close to their natural environment as possible, why not give it a go? People have to learn by trying or nothing would ever be known, right.. I would just be weary of the chams possibly drowning if they fall or venture. Id o not know what mudskippers are, but hope that their diet wouldnt involve a pygmy if it was readily available.. Good luck to ya.