Note that drop-off fees aren't always listed separately. I have found cases where a rental from City X and taking it to City Y simply had a higher base rate than for a rental starting and ending in City X.
-I typically check the major rental companies, including Budget, Avis, Hertz, Enterprise, etc., using any discount codes I can use, including those from Costco, my credit union, airline frequent flyer programs, and AARP, to see which will give me the biggest discount. On one recent trip, I used both AARP discounts (for Enterprise) and American Airlines frequent flyer discount code (for Avis). One friend said he got a great rate for San Jose-San Diego using the Southwest Airlines Web site.
-It can also be worthwhile to check cosolidator sites such as Hotwire, Priceline, etc. Some have reported that rates go down as the date of the rental gets closer. I haven't found that to be true, but they could be right in some cases.
-In many, though not all, cases, you can save some money by renting at an off-airport rental location.
There's always the train.