There's the obvious answer: what do you want to look at on or under your desk for the next few years and beyond? Whether your PC goes on top of your desk is also a big factor in deciding case size. However, there's some more technical gubbins to be aware of here.
First is motherboard support. There are a range of sizes of motherboard, but they're standardized. That means if a case says it supports a size, you shouldn't really run into any issues. The sizes, from largest to smallest, are:
E-ATX / ATX / M-ATX / Mini-ITX
The good news is that most PC cases that support, say, an ATX motherboard, also support the smaller motherboard sizes too. So M-ATX and Mini-ITX should fit just fine.
One other thing to consider with motherboards is whether you plan to use a new technology often called Back-Connect, or BTF. These motherboards, made by MSI and Asus, stick the connectors on the rear of the motherboard for a neater look. It's a good effect, too, though you will need a case that explicitly supports this sort of set-up.
The other things to consider when sizing up your PC case are PSU size, GPU size, and cooler size.
When it comes to PSU size, most are built to the ATX standard and most cases fit these. However, there are the SFX and SFX-L standards for smaller, usually Mini-ITX builds. You can usually check whether a case supports a certain length of PSU in the product specifications. Generally, it's a non-issue.
GPU size is a simple check: just measure your GPU and check whether your case can fit that. Again, a case's product page will usually cover this. Some cases are more limited than others in this regard, so it's definitely worth checking with today's huge graphics cards.
Cooler size matters whether you're buying either a liquid or air cooler. For a liquid cooler, you need to check whether there's room to mount a radiator of your chosen size inside the case. Ie. a mounting point for a 360 mm radiator close enough to the CPU for the cooler's tubing to reach. For an air cooler, you need to make sure your case supports the height requirements of the cooler. You don't want to install everything only to find your tempered glass side panel hits the top of your CPU cooler.
The good news is, most ATX compatible cases are made with making this all pretty straightforward. They leave more room than most will need, so providing you're not going over the top, you're likely going to be just fine.