"The hell with the rules. If it sounds right, then it is." -- Eddie Van Halen
I use whatever the song calls for. I've tried dry DI through an Edirol or Behringer box with various plugins, reamping with the FM3, using full wet effects (tasteful and never too much) from my FM3 in mono or stereo, and all of the above. All have their place and really can make or break the guitar sound. Fortunately, during the demo or scratch track process it's fairly easy to try the different tones and determine what works best for the song or group of songs that I'm working on.
Lately, my FM3 is just perfect for the sound I want. To my ears, it's just more authentic and organic sounding. I'll often start with a preset and tweak slightly based on the guitar I'm using, plus try different IR's. I also experiment with high/low cuts in the cab block vs. in the DAW. I kind of like doing it in the DAW so that when I'm mixing I have more control over finding the frequency cut sweet spots and then notching down some of the competing frequencies in the mids.
Sometimes, plugins are better for a song. I've already spent way too much on guitar plugins including Neural DSP, Audio Assault, Plugin Alliance, Bogren, and Amplitube, but it's nice to have options. The Neural plugins seem to have a lot of hype behind them, but really do sound quite good most of the time. And they come with some really good presets which shortens the tone tweaking process. I also picked up the Bogren one knob plugin which I find sounds pretty bad on it's own but often really good in a mix.. (imagine that?!)... and the Rockman from the Amplitube Joe Satriani collection usually sounds great when filling out a guitar sound or when nothing else seems to sound right.
FWIW, after many years of home recording I have found that the recordings that age the best are the ones that, 1. were mixed listening both in mono and stereo (so they are more balanced and transferrable across different audio systems like car, home stereo, USB device, boombox, etc., 2. have less gain on the guitars (less is more), and 3. were mixed at higher and lower volumes on a nice set of studio monitors (I use the Kali LP6's). My ears also tend to love guitar and drums. So I have to check myself and make sure neither overpower the mix. Nothing tires my ears more than the guitars or drums being too loud.
Anyway, hope this has some value.