Is it a best practice to install programs to Program Files?

While not an official source, Raymond Chen at The Old New Thing has discussed this.

Specifically, the above-linked blog post states:

Some of Microsoft's software certification programs (such as the Windows Logo) require that applications set their default installation location to the Program Files directory.
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Program Files was introduced in an attempt to bring order to chaos. Think of it as painting lines in a parking garage.

Naturally, compliance with those software certification programs' terms would only apply if you intended to apply for (or already have applied, and received certification under) those particular software certification programs. And more to the point in this case, it's about the default installation path, nothing more.