Let's face it, you're not going to find a centrally located hotel with five-star services for a budget price. You're always going to face a trade-off between three factors: price, location, and amenities. If you're clear about your priorities, you're more likely to be satisfied with your final choice.
Price. Decide the maximum amount you're willing to spend on a hotel. Are you trying to stretch your dollars so you can stay on the road as long as possible? Or is this trip all about comfort and luxury? Are the costs coming out of your pocket, or is the company paying the tab? You might consider beginning or ending your trip at a luxury establishment, and spending the rest of the time in more modest digs.
Location. Is the hotel near restaurants, shopping, beaches, and so on? Is it convenient to the activities you've planned? Is public transportation available? How about reasonably priced parking (if you have a car)? Don't get stuck miles from the action, unless that's really what you're looking for.
Amenities. Do you require an in-room Jacuzzi? Or is the simple absence of bedbugs sufficient for your comfort? The more extras you require, the more you're going to pay. But remember, creature comforts can be especially important when nerves are frayed by travel, so consider investing.