We explore various prospects of using gravitational wave (GW) detectors to probe beyond-the-standard-model (BSM) physics. First, we formulate an explicitly gauge-invariant observable for any general gravitational perturbation, not necessarily due to GWs, in a laser interferometry-based GW detector. This is done by computing the proper time elapsed as measured by the beamsplitter. We demonstrate that, for a plane GW, the proper time observable is equivalent to the detector strain commonly used by the GW community, but this approach easily generalizes to other types of signals. We then apply the proper time formalism to three notable physics cases: 1) transiting clumps of dark matter, 2) fluctuations of gravitons in an EFT vacuum, and 3) quantum gravity fluctuations at the horizon of a causal diamond (i.e., the Verlinde-Zurek effect). In particular, we will make some intriguing observations regarding gauge invariance and negative-norm states in a very recent paper by Carney et al. (2409.03894), which computed the signal in case 2. Finally, we introduce an analogous gauge-invariant observable for atom interferometers and discuss its implications for GW and dark matter searches.