According to Table G3.1 in ASHRAE Std. 90.1, Appendix G, "for existing building envelopes, the baseline building design shall reflect existing conditions prior to any revisions that are part of the scope of work being evaluated." For all other elements besides the envelope - including HVAC systems, hot water systems, lighting, etc. - the modeling assumptions for the baseline building are the same for existing buildings as they are for new buildings. Please review Table G3.1 thoroughly for guidance on how to model the baseline building.
Updated 10/1/13 for rating system applicability.