The Spark and Yaris are tiny and generally regarded as not that safe. Not sure where you're commuting but if there isn't a lot of city driving, not sure the size tradeoff is worth it.
Other than that, there are quite a few good options out there for simple, reliable commuting. How much do you like to drive? Is handling, power, important to you?
The Ford Focus will lean to the sporty side, while being fairly refined and comfortable. Some don't agree with the (in my opinion) super-awkward center console and poor built-in computer system.
The Mazda3, another reliable option, will also be sporty. It'll focus less on gadgets and more on the ride and drive. Arguably more reliable.
The Kia Rio is also going to be reliable, with a middle-ground between handling and comfort.
The Honda Civic is somewhat of a benchmark. It's fairly 'boring' but will get you from a to b every time, all the time.
The Toyota Corolla is like the Honda, with some more interior gadgetry and even less of a driving experience.
I'd recommend staying away from 4-year-old GM cars right now. :p
My recommendation is to drive 'em, see how you like them. Like I said, plenty of options, and it will mostly come down to personal preference.