A couple of things

[JACSUK_999]

Can we have an option to make some rooms invisible to certain people (i.e. only SA can see, and then tick boxes for others etc) and this needs to apply to the php tracking code to.

An option to make our own skins?

Invisible mode for SA’s and maybe the option for CA’s to.

Ability to hide server.

Mute play from all other players, just in case you don’t want to kick them, but would like to mute them for a bit… (as I understand it the current mute thing is for u only…) or like a time-out thing where u mute them for a bit as like a punishment…

I have more but will have to add them later as I can’t think of them right now…

[woutur]

Can we have an option to make some rooms invisible to certain people (i.e. only SA can see, and then tick boxes for others etc) and this needs to apply to the php tracking code to.
Why would you want it? Just password those channels.

An option to make our own skins?
No, TeamSpeak has a nice look :)

Invisible mode for SA’s and maybe the option for CA’s to.

No, this has been discussed extensively before, and NO was the conclusion.

Ability to hide server.
It's already in.

Mute play from all other players, just in case you don’t want to kick them, but would like to mute them for a bit… (as I understand it the current mute thing is for u only…) or like a time-out thing where u mute them for a bit as like a punishment…
You can achieve this by moderating channels and take away the voice flag of these people.

[Peter]

Well,

from the points you mention the "invisible serveradmin" will NOT be done (as wouter said) - and the "hide server" I frankly have no idea what you mean =).
But all the other things you ask for should be doable with ts3, if all goes well :).