I'll list some I sorely wish had gotten more time to produce an ending:
* The Negation War - I wasn't that much of a fan of many of the stories within the CrossGen universe but The Negation was superb, I loved the characters and the story (and having a normal human be a more effective leader of a bunch of supers was fantastic)... a great idea to have so many different stories merge into one all out war and then poof... the series is cut short
* Stormwatch Team Achilles (I know they got a bit of a quick reference some years later but... I still feel cheated). The character writing on this really drew me in, not to mention the idea of a bunch of regular humans dealing with an SPB world and mostly getting away with it on many levels with just exploiting simple weaknesses
* Pirates of Coney Island (I ran into the creator a couple years ago at MoCCANY and he mentioned he eventually wants to finish the final two issues but that was at least a couple years ago and the series hadn't had a new issues in at least another year on top of that). I loved the colorful art of this series and just as the story was getting interesting...
* Highway 13 (I don't think there were many issues left in this series and it ended on a cliffhanger
* PS238 (I really don't know what's going on with this series but there were storylines still left unfinished). The saddest thing is this is quite possibly my favorite comic series out of anything I own, I found myself loving it more and more with every issue and then supposedly the creator was going to just publish it online but from what I've seen leaves me thinking this series is done.
* Circles (supposedly it's an issue of the artist not having time... and supposedly this one will eventually wrap up). They had gotten a little past the halfway point on this series and certain major events were mapped out.
* Coyote River (apparently lack of time on the creator's part to bring this to an end).
* Thieves and Kings (I haven't read much of this series, partly because I don't like how it's unfinished - supposedly it had a set number of issues which were going to be published and only got halfway there).