Your question stirs a lot of emotions! Personally, I can't think of much that would make a yard nicer than having a prairie dog town in it! What fantastic entertainment, courtesy of Mother Nature! And no landscaping or watering required. A dream come true, not to mention a great opportunity to set an eco-friendly example for the entire neighborhood. A "nice" yard can mean anything YOU want it to - all it takes is a little change of perspective and priority.
Let's step back for a minute and look at the bigger picture. The Black-tailed Prairie Dog is currently a candidate for federal listing as a Threatened species. The State of Texas has committed itself to a goal of just under 300,000 acres occupied by the species by the year 2011. This figure represents only 1% - yes, 1% - of the original habitat of this species. The prairie dog may not be endangered - yet - in your area, but that's exactly what makes your area so critical to the species' survival. Even if the prairie dog gets 1% of its habitat back, that means we have the other 99% - so who's the "awful pest"? Are you passing judgment on prairie dogs because they don't do anything more constructive than "make holes all day long"? What they're doing is all prairie dogs need or know how to do, and it certainly is not our place to say it isn't good enough, now is it? Honestly, if you're going to seek sympathy and constructive advice from a wildlife biologist, you'd be better off couching your questions a bit more diplomatically!
Stray dogs and cats - and humans, for that matter - are in absolutely no danger of extinction. One could make a valid argument that prairie dog lives are MORE valuable because they actually contribute something to a healthy ecosystem. What more can one ask of a species?