Large Language Models (LLMs) are widely used in software engineering (SE) research and practice, yet their non-determinism, opaque training data, and rapidly evolving models threaten the reproducibility and replicability of empirical studies. We address this challenge through a collaborative effort of 22 researchers, presenting a taxonomy of seven study types that organizes how LLMs are used in SE research, together with eight guidelines for designing and reporting such studies. Each guideline distinguishes requirements (must) from recommendations (should) and is contextualized by the study types it applies to. Our guidelines recommend that researchers: (1) declare LLM usage and role; (2) report model versions, configurations, and customizations; (3) document the system and prompt design beyond the model; (4) report session traces, i.e., interaction logs and runtime traces; (5) use suitable baselines, benchmarks, and metrics; (6) include an open LLM as a baseline; (7) validate LLM outputs against human judgment; and (8) articulate limitations and mitigations. We complement the guidelines with an applicability matrix mapping guidelines to study types and a reporting checklist for authors and reviewers. We maintain the study types and guidelines online as a living resource for the community to use and shape (llm-guidelines$.$org).