Depends on what I'm using it for.... Caliber is a tool, like anything else. I view it sort of like saying, "Do you prefer metric or SAE tools?" or, "Do you prefer slotted or phillips head screwdrivers?" It depends what you need it for.
I have more 9 mm handguns b/c cost was a significant factor for me when I started shooting (and still is). I've kept them b/c the cost allows cheaper practice, I like my 9 mm platforms, capacity is higher, and availability is top notch.
I also love .45 ACP. I shoot it very accurately, I like the added power, and with the XD 45, I can get 13+1, which rivals a lot of 9 mms out there.
If it came down to it in a SHTF scenario in my home with both in the safe, I'd grab the .45 ACP for the added power. That said, I carry a 9 mm a lot. I now use .22 LR for most practice when I can b/c it's a LOT cheaper and still fun.
If I could have an unlimited supply of handgun ammo for life in one caliber only, I would pick 10 mm full house loads.