What would it be? I mean ship classes, rather than specific mods people have done - there're way to many of those that probably deserve to be canon to list them all.
As for myself, I actually have several I'd like to see, mainly for FREDding purposes - I've often wanted a very specific ship class but never been able to find one - My top three would be a light GTVA installation, a light Terran carrier, between Corvette and destroyer in size, and a Large Vasudan transport, pretty much in that order.
They'd all be useful, but a light installation'd open up a few more stories I think - It'd be useful as a civvy base, or as a research centre, or a frontier station, etc. etc. A light carrier'd be cool as a sort of stepping stone in opposing forces - something that's a challenge, but not quite destroyer level, but the installation wins because ultimately it'd be a little more versatile IMO.
If you could add one ship to canon
1TI - Coming in 2011 - Promise!

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"Everyone has to wear clothes, and if you don't, you get arrested!" - Mr. T