I do this with some regularity. Here's how I see it - $50 or $100 is an appropriate incentive for the front desk employee to find me the best room that he possibly can. It's not encouraging "breaking the rules" - I really think it's unlikely that front desk staff would be willing to do anything that risks them getting fired over $50. Sometimes a manager has to be consulted and they have always been fine with it.

If the clerk can offer me an upgrade to an unoccupied room, then it's really a win-win situation for all involved. I become a very satisfied customer, the clerk gets a bonus, and the hotel doesn't really incur any additional cost except for possibly a marginal increase in housekeeping expense.

I will note that I don't try this in places where I know it to be against the rules - i.e. Wynn and some other Las Vegas properties.

Specific examples - this year I received an upgrade from a city-view room to an oceanfront room with a huge lanai at one of the oldest and best hotels in Honolulu. And received an upgrade from a regular room to a huge, 2-bedroom flat at one of the newest and hippest hotels in Ft Lauderdale. Both times the upgrade was not essential but very much appreciated. If I absolutely need a specific type of room then I will book and pay for it.