There are several factors which, in my opinion, must be considered when making a decision on what to do:
Both hot- and cold-aisle containment require that you have either one row of racks, with a wall on the other side; or you have two rows of racks, both of which are of identical length and are aligned properly. This makes a long, thin room better for hot- and cold-aisle containment.
Is your environment going to have a raised floor, or (probably the more apt question) does it already? If you go for hot-aisle containment with a raised floor, you'll going to have an interesting time getting the hot air returned to the air handlers units. I think you'll also need a way to ensure air circulated in the under-floor area.
* External heat sources
Lighting and people impose an additional heat load, for which you must account. The same applies to the UPS. Also, don't forget about all of your networking equipment and patch panels that prefer living in two-post racks.
If I remember hot-aisle continment theory, the cold air being ejected from the in-row air handlers doesn't get very far into the room before it is pulled in to the servers in neighbor racks. If that is the case, and your room is big enough -- with enough space between rows and stand-alone equipment -- then you might end up with a hot-aisle-containment environment where the stand-alone equipment sits in a little hot spot, unable to draw any cool air from (relatively) far away in-row air handlers.
* Cooling Source
Most of the time, when you think of a data center, you think chilled water. That is not always the case, and I'm not talking about this newfangled stuff like using outside air. I mean some buildings simply don't have the capacity (in whatever way you want) to support the chilled-water needs of a data center. You might have to rely on an air-cooled solution.
You have to maintain humidity as well as temperature, and the humidification/dehumidification equipment takes up alot of space. When you're going for hot-aisle containment, you're likely going to use in-row air handlers. You want these to be as compact as possible, so plan on getting a separate unit to handle the humidity.
If you're doing cold-aisle containment, you're likely going to use stand-alone air handlers, which will include humidity control already.
All of the thoughts above were going through my head in the last 12 months. In the company where I'm working, at the start of 2010, it was looking like we were going to move into a new building. At the time, the building was an empty shell, so a data center was designed that was long (to get two aligned rows), thin (so no areas for hot spots to build up), and with no raised floor (to save the expense). We were going to go for hot-aisle containment, in-row cooling, in-row UPS, and a little stand-alone device for humidity control and backup cooling. The move was cancelled, so we started over. Besides, we learned towards the end that it would be air-cooled, not chilled water (in other words, bad).
The new plan would be to stay in our current building, extending part of our existing data center (standard raised floor, stand-alone chilled water cooling) into a space that would still give us two long rows, but the raised floor and chilled water availability -- along with the ability to re-use existing air handlers -- make me want to go cold-aisle containment. Unfortunately, that was scrapped as well.
In the end, it looks like we'll simply be taking down some existing walls in our data center, giving us several rows of racks, all of which are not aligned. Hot- and cold-aisle containment now looks impractical, unfortunately, but I did learn alot while doing my research. This move will also give me the ability to change out the hodepodge of racks to newer, deeper racks (one thing that can really help is to keep cables out of the way of the back of the server), and to install blanking panels over every open rack U (again, another easy way to keep hot and cold air mixing). I'll also be asking if it will if some of the ceiling tiles are changed out, replacing solid tiles with grates, allowing more hot air to float up into the plenum.