.45 Colt is a bigger case, and given a strong revolver can be loaded to beyond the .44, and, is better with heavy bullets.
The .44 mag can be easily downloaded using .44 Special. It's also seeing near the same potential as the heavy 45 Colt loads with heavy bullets, and some of Buffalobore and Garett's loads. If you want a good idea of what both cartridges are capable, Buffalobore is a good place to start.
Heavy 45 Colt +P Ammo - 260 gr. J.H.P. (1,450 fps/M.E. 1,214 ft. lbs.)
Heavy 45 Colt +P Ammo - 325 gr. L.B.T.-L.F.N. (1,325 fps/M.E. 1,267 ft. lbs.)
Deer Grenade .44 Magnum +P Ammo - 240 gr.Soft Cast - G.C. (1,550 fps
Heavy
.44 Magnum Ammo - 305 gr.L.B.T.-L.F.N.(1,325fps/M.E.1,189 ft.lbs.)Heavy .44 Magnum Ammo - 270 gr. J.F.N. (1,450 fps/M.E. 1,260 ft. lbs.)
Heavy .44 Magnum +P+ Ammo - 340 gr. L.F.N. - G.C. (1,478 fps/M.E. 1,649 ft. lbs.)
"The .454 Casull is one cartridge that Buffalo Bore Ammunition does not load to it's full pressure limit. When loaded to it's full pressure potential the .454 Casull can become unreliable and unpleasant to shoot. At upper pressure levels, heavy bullets tend to jump crimp - tying up the cylinder. (wouldn't this be great in an emergency) Also, fired brass can stick in the chambers. "
454 Casull Ammo - 300 gr. J.F.N. (1,650 fps/M.E. 1,813 ft. lbs.)
454 Casull Ammo - 325 gr. L.B.T. -L.F.N. (1,525 fps/M.E. 1,678 ft. lbs.)
454 Casull Ammo - 360 gr. L.B.T. - L.W.N. (1,425 fps/M.E. 1,623 ft. lbs.)
Bottom line is what gun do you want, how big, and do you want a 5 or 6 shot?
CraigC had an excellent point. .44's tend to be made to tighter specs, and with more room for error. Also, the cylinder for the .45 is bigger, so to get a strong, tight cylinder usually either means a 5 shot, .454, or a custom.
Also, do you handload? It's worth checking the prices of the ammunition for either gun, and what you intend to shoot with it.
You'll notice that the "Deer Grenade" .44 magnum by BB is a 240 grain bullet at 1550fps. At lower pressure, the .45 Colt 260 grain bullet hits 1450 fps.
That sums up the discussion in a nut shell. .45 Colt gives you more bullet weight, at near the same speed as the .44 magnum, with less pressure.
You might just read John Linebaugh on the subject, here:
http://www.customsixguns.com/writings/dissolving_the_myth.htm
If you look at the bottom, Linebaugh uses cast bullets, between 260-320 grains, at moderate velocities, 900-1280 fps. His main hunting load was, IIRC for deer, 260 grain cast at 1200 fps, using H110.
I settled on a 260 grain HP at 1450 fps. I found, without custom grips, this is as much as I want to shoot. I had a bunch of 325's at 1350 fps.
Quite the handful, and, my custom did digest 360's at 1550 fps. Just to see what a cape buffalo load was like.
Finding a strong, well made gun is easier with the 44.
BFR makes a beautiful .454 you could use for .45 Colt, or just stay with .45 Colt.
http://www.magnumresearch.com/Expand.asp?ProductCode=BFR454C7