I've started to standardize on the WM house brand, which is currently made by Johnson Pumps. Why? Because they tend to have a high failure rate and WM will replace them with a no-questions replacement from store stock, and there's a WM not too far from wherever I sail. I like the WM/Johnson solid-state bilge switch too (no moving parts and it mounts right to the pump with a click).

For holding tank pump-out I went for the most reliable I could find (a Dometic SaniPump) because that's a job I don't want to do again as long as I own this boat.