We describe a combinatorial model for the $q$-analogs of the generalized Stirling numbers in terms of bugs and colonies. Using both algebraic and combinatorial methods, we derive explicit formulas, recursions and generating functions for these $q$-analogs. We give a weight preserving bijective correspondence between our combinatorial model and rook placements on Ferrer boards. We outline a direct application of our theory to the theory of dual graded graphs developed by Fomin. Lastly we define a natural $p,q$-analog of these generalized Stirling numbers.