In real aviation how is the Direct GPS used in flight plans if used? ???

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...have to disagree with you on that one Ozzy  At least the case is such here in the States. If it's late at night, I often do file direct on the flight plan, and usually with the exception of a fix or two, get it! I'm talking Toronto to Fort Lauderdale in some instances! Something to keep in mind though, I usually only do this late at night(2400 or later). As a  matter of fact, you can even file direct in a non-GPS equipped A/C, as long as the distance doesn't exceed the route MRA. Sometimes doing this is even a necessity. A real world example would be KFLL to KAPF. If you use Victor airways it'll take 114nm, and if you go direct, 88nm ! !  If I'm in a Cherokee, unless I'm time building,  I'm going direct! 
As far as answering your question KnightHawk, the verbage on the flight plan isn't any different. Most airways are still based on VOR radials(the "Q" routes going over the US Gulf of Mexico, and the "Blue Spruce" routes (Atlantic long distance)would be just two exceptions). In the example I gave at the top, I might file (   RSW   APF ) on the route section of my flight plan. What this is interpreted as by the person accepting the flight plan is: direct RSW-vor  direct Naples-vor direct. How does GPS tie into this..............A/C EQUIPMENT code.    ie: 172/G in US format or SDG/C in ICAO. 

Excellent point! I was going to mention that, but I didn't want to write a book!     If I can, I like to fly as high as possible, for several reasons. One of them being lower traffic density, which obviously spells more options for ATC.     Being as high as possible isn't always the answer(in regard to GPS direct routing). Sometimes the low altitude guys can be alone "down there". A good example is here in Florida. I always hear the Flight Express(Cessna 210's and Barons)  guys receiving "direct" clearance as soon as they check on with Miami departure. That's about a minute or two after takeoff!     But, again, this usually occurs after midnight. Knowing your route(is it on or parallel to airways or ATC corridors) and reading the controllers mood are two big factors when requesting an "enroute" direct clearance from ATC. It cracks me up when I hear "how about direct Waterville for Delta's 989?!". You just know a, what I call the demand/request, is gonna rub the controller the wrong way. For future reference, place the above mentioned example in the"How not to do it" file!
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Tonight I flew from Destin KDTS to KFLL. I heard Jacksonville Center clear a United flight "direct Corona (CNX-VOR) direct 29Palms (TNP-VOR) direct".  If you check your charts, that's from North Florida, "direct" New Mexico, "direct" Southern California and then "direct" once more!  Just out of general interest, MYrouting was [ KDTS (dir) PNS (dir) VRB (dir) ZFP (dir) ZBV (dir) DEKAL (dir) KFLL ] and I flew at 410. 

Yep! This is when you realise that this is,after all, only a sim.