"Best" is always subjective and brings about a lot of opinions, often based on personal preference, so I never like when people ask about what is "the best." I'm a former Nissan Master technician and I can tell you what "I" use on my 2006 LE and what "I" have done to it. I'm not saying everything I use or did is "the best," but is what works for me and what upgrades I chose to do after a lot of research, in some cases:
Genuine Nissan oil filter and Walmart SuperTech full-synthetic 5W30 oil.
Valvoline Maxlife ATF used in the automatic transmission and the AUTO-mode transfer case.
Walmart Supertech full-synthetic or Mobil One full-synthetic gear oil in the front and rear diffs, 75W90.
I don't use fuel additives.
Spark plugs: NGK PLFR5A-11 spark plugs (original equipment)
Tires: Michelin LTX MS/2's. This was the first set I had on the vehicle and it will be the next set. I currently have Nitto Dura Grapplers which are a very good tire, but they ride much harsher than the Michelins. Most of my driving is on paved roads and highways.
Suspension: KYB GR2/Excels front struts. Bilstein HD rear shocks. Airlift 1000 air bags.
Engine: Extreme performance intake spacer. An aFe Momentum air intake system with dry filter (it's expensive, though). Stillen standard size, aluminum crank pulley (which I still debate was worth the money).
Exhaust: Dough Thorley shorty headers. Dough Thorley mid-pipes (which replace the rear cats). Factory muffler cut out and replaced with a Magnaflow #12580 muffler (some pipe fabrication was necessary as it's a 2-IN/1-OUT design.
Tuner: Superchips Flashpaq using the 93 Performance tune, 3-degree ignition advance, raised limiters on RPM and speed. There are probably better choices for tuners, but I got this one for a good price and did what I wanted, except for one thing: the latest software does not have the disable feature for the WOT restriction. Bully Dog and Hypertech tuners still disable the WOT, if I'm not mistaken. If you are looking to get "serious" and do custom tunes and dyno runs, UpRev is probably the best way to go.
The changes definitely made a difference in performance! Gas mileage, if I can keep my foot out of it, is about the same. The exhaust, mainly the muffler, take several hundred miles to break-in. After 1000 miles, it has a nice rumble at idle, sounds great wide-open in the 2500-3500 RPM range, but does has a considerable "drone" during "regular" driving conditions. I did start a thread on my upgrades, but haven't had time to update it in a while (I really need to get back to it). Just do a search for "Blueprint mod" and you should be able to find the thread.
As far as floor mats, Weathertech and Husky have some nice options.