First of all, let me specify that we are talking about Domestic here, as international is a different (and generally higher CPM) game.

IMO, the number of permitted transfers is really not all that important for the MRer after EQM; only the MRer who is after segments needs to pay a ton of attention to transfer limits.
Why? Because with a goal of EQM, adding segments is not very time efficient compared to longer flights in the right order. For the segment runner, what you want are ultra low fares ($60 or less base RT) that allow lots of transfers, but that is not the most important restriction: the routing rules need to allow routing through several cities that are currently flown with schedules that allow this transfer in a timely manner. The majority (but not all) ultra low sale fares specify a non-stop routing or a single connection option. These same fare may also say "transfers: up to 4 each way" permitted, but the routing rules usually restrict you to less than this.

Take a good look at the routings I chose in my response to you here.
The key to these routings are not the # of transfers permitted by the fare (usually fare more than I choose) but rather the cities that are allowed to be transited and in what order.
In Example 1, I only transfered once each way and the routing provided 6445 EQM on the routing flown versus 4908 EQM non-stop....but the routing was chosen for efficiency and comfort. 6445 EQM per day, day after day. You are not going to get that with segments.

In Example 2, I transfered twice each way. No more, but flew 8277 EQM instead of 4266 EQM, the non-stop distance. This itinerary took 27 hours and you are not going to get 8277 EQM in 27 hours just by padding segments.

The key is the order you are allowed to transit where. This post on routing rules may be helpful to you.

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Basically, my primary method to find MR fares is:
1) Go to FareCompare and search from your city sorting by price.
Open up a separate browser and look up the routing for each interesting fare on FareCompare.
Don't book anything most days.
2) Keep going to FareCompare everyday until one day an unusually low fare with a juicy routing comes along. After exploring availability and best schedules (on the longest routes permitted by the routing rules) book with haste. The better the fare, the less likely it is going to stick around for long.