Fit and comfort are most important, so if you can be happier with different handlebar tape or grips or a saddle or a stem that makes the fit better, that's all worthwhile.

As others said, tires. They're not sexy, and they're not as well understood as the other components of the bike, but they're critical. Nice tires make a nice bike.

And that's about it. There are occasionally good reasons to upgrade. As some say, wheels can be a worthwhile upgrade.