As of now (and this may change due to bankruptcies), Delta has a partnership with Hertz where PMs and DMs get free Hertz President's Circle, which is their highest tier. With that, I've also matched to National for Emerald Club Executive Elite. At this point, I just book whichever is cheaper and/or available and snag a car from the PC or the Executive Aisle. National probably has the slight edge overall, but if I'm paying with my money I consider myself a free agent.
Hotels are a bit different, and it depends a lot more on your destination. With the SPG merger into Marriott, the best hotel program to be a member of (in my opinion) is probably Hyatt, but they also have a relatively small radius. I frequently find that Hyatt doesn't have a hotel where I'm going, or has a significantly worse property selection than the other big chains.
There is some synergy here with credit cards as well - Chase URs transfer very well to Hyatt (probably the best way to earn hotel points from a general purpose "travel" CC), so I often find myself with an extra bias towards Hyatt due to the URs that I've saved up.
IMO, the *points* portion of rental car loyalty is basically hot air, and Hotels have been trending that way (but are not as bad). Loyalty tiers are still valuable at both, though, so I would optimize for that first and foremost. There's no point choosing loyalty to Hyatt if the Marriott is the property you want to stay at every week, and vv.