I would say do what ever flops your mop... I have both 44 Magnum, and 45 Colt (not long Colt), in rifle and pistol...
The main thing to do is choose a bullet style that feeds well in your rifle.
Bill
I just knew I'd get my hand slapped for the word, "Long".
So, okay, since you have both... maybe both in the leverguns... and maybe maybe maybe both in a Marlin lever... which one would you grab first? And why?
I was reading an article by Steve Lee,
http://www.leverguns.com/articles/lee_marlin44.htm "Magnum Marlin, My .44 caliber friend", and he says that the .44 Magnum is his rifle to grab first. However, most of what he says in the article could/might apply to the .45 Colt just as well as to the .44 Mag.
Probably some of the SASS / cowboy action shooters have one or the other as a favorite, but there again, most of the cowboy action shooting is done with tamer loadings... which I'd be shooting myself for plinking or casual target practice and fun. After all, most of our shooting is, indeed, for fun. I've even been thinking to go out to the range and see what this cowboy action is all about.
Just thinking that some more businesslike loads are good to have, too, and that is a consideration. Logically, both cartridges ought to be able to run out some hot loads from the Marlin, but I wanted to be sure on that one as well--case strength is a limiting factor on the .45 Colt I think. (?) Certainly the Colt has it all over the .44 Magnum for nostalgia and history...
Keith