I'm currently trying to choose between the 2 myself, so here's my current take.
45 colt:
Pros:
It's classy
It's a quintessential cartridge
Can be loaded up to 44 mag levels (some say beyond, others say less than, Hodgdon's website says less than....)
Lower pressures (For whatever it's worth)
Slightly larger diameter
Cons:
You essentially have to reload if you want to make full use of it
If you own non ruger 45's, you have to be very careful where you put your magnumized loadings.
fewer bullets and such available
The difference between "the gun can take it" and "the gun was designed to take it"
44:
Pros:
It's a quintessential cartridge
lots of choices in bullets
heavy hitting factory ammo readily available
44 guns supposedly tend to be manufactured slightly better (dunno how applicable that is in a blackhawk to blackhawk comparison though)
better sectional density at a given weight
Cons:
Not terribly historic
slightly smaller diameter
Sounds scarier in court if you ever use it to defend yourself against a human attacker
Some additional reading if you want:
http://www.customsixguns.com/writings/dissolving_the_myth.htm
http://www.chuckhawks.com/high-pressure45.htm
http://www.familyfriendsfirearms.com/forum/archive/index.php/t-42402.html
http://www.handloads.com/articles/default.asp?id=5
http://www.lasc.us/Fryxell44OverWeight.htm
Also, a search here on thr will reveal a couple more threads on this topic, and a google search, of course, reveals even more. My own non-expert opinion is that the 44 has a slight edge in terms of biggest boom and general use. But the magnumized 45 is a little more classy.
I really wish someone made an affordable 454 single action.