Favorite ship: The Colossus. It . . . it's just the COLOSSUS. 'Nuff said.
I'm going to go for the Colossus as well. The Guardian Angel is a fine ship, but at the end of the day, I was thinking of it for it's crew, not the ship itself. Sorry Crystal and co...

So I'm taking the Colossus. Apart from the obvious fact it's a beast of a ship, there's the way it's built up. From literally through the Colossus Cutscene to the fact it's built up as everything depends on the Colossus, as it displays it's power in numerous engagements, and even brings down the first Sathanas (with a lot of help.) I also like the fact it's crew don't just try to beam everything to oblivion which would be the easy thing with a ship like that, they try to reason with Koth first, before blowing him and his crew to dust. So then when the Colossus finally goes down, it's a memorable moment.
And of course, let's not forget about the baseball bat swing. I'm surprised (unless it hasn't already been done) that no one has made a mission of the Colossus just swatting fighters like flies with the "bat"!

Let's finish this up with the Colossus Cutscene. 20 years to build, all the major corporations, Terrans and Vasudans...