I also think replacing countertops can give a kitchen or bath a whole new feel without replacing everything. 

What countertop are you putting in?

Sometimes when someone does gray carpets, gray walls, gray countertops etc it becomes a gray overload in my opinion though!

Pay attention to the little things: faucets, cabinets, cabinet hardware, ALL floors (not just the carpeted areas) light switch covers, outlet covers, sinks, baseboards, counter tops, light fixtures, these small things can add up quickly in material and/or labor costs.

I decided to do some cosmetic updates to the house while I am in it (new flooring, paint, appliances, counter top then staged it with new furniture) all with the idea to flip it.

I'm not doing any cabinets or countertops at this juncture, I will be painting cabinets in some units and replacing hardware, making paint uniform in color, and flooring uniform in material throughout the units so they simply flow and show better, minimal fixture and covers/plates work.

If I put $15,000 of rehab into each unit, installing modern rental-grade cabinets, granite countertops, nice laminate flooring, stainless steel appliances, modern light fixtures, new plumbing fixtures, etc., is that worth getting $250 extra rents per unit?

Money is probably best spent on fresh paint then flooring and/or countertops....anything a deep cleaning doesn't bring up to a clean look.

More like putting in new cabinets, sinks, and new countertop in the kitchen. 

I have some offers out for apartments that need some cosmetic updating (tile flooring updates, kitchen/bathroom countertop updates, and some handiwork - replacing doors and closet doors, etc.).