One that randomly hits me is:  Paying a realtor a 3% sale commission ($15,000) on sale of a $500k property.  

Real estate broker'', hereinafter referred to as broker, any person who for another person and for a fee, commission or other valuable consideration, or with the intention or in the expectation or upon the promise of receiving or collecting a fee, commission or other valuable consideration, does any of the following: sells, exchanges, purchases, rents or leases, or negotiates, or offers, attempts or agrees to negotiate the sale, exchange, purchase, rental or leasing of any real estate, or lists or offers, attempts or agrees to list any real estate, or buys or offers to buy, sells or offers to sell or otherwise deals in options on real estate, or advertises or holds himself out as engaged in the business of selling, exchanging, purchasing, renting or leasing real estate, or assists or directs in the procuring of prospects or the negotiation or completion of any agreement or transaction which results or is intended to result in the sale, exchange, purchase, leasing or renting of any real estate.

If that time impedes your W2 career development, takes away a sales commission in the “day job”, etc. you can end up with a bad return on your time.

This is assuming the purchase price is $1M and the commission is 6%. 

I don't mind splitting commission for like $4k when the deal only takes like 2 weeks to close.

This is an off market transaction and no commissions are due.

If I were in your situation I would increase rents to market (or close to market) per sq. ft. costs (maybe give them free months rent or reduce slightly if you will not have to pay any TI or broker commissions) without increasing their square footage.

Similarly, if you double close are you expected to pay commissions on each close?

Yet commission rates are untouched.  5-6% is still standard.  

(Judd) Absolutely, I would be happy to get some extra work,  I'm currently a window cleaner for Fish Window Cleaning which is commission based and flexible scheduling, making it perfect for college but the temperatures just dropped below freezing and we usually slow down quite a bit during that time, if you have some work that would be great!