I use various methods of recording guitar. For the most organic results, I'll use amps and cabs set up in the iso booth, played at a volume that the amp sounds good at. With higher powered tube amps, this volume can be pretty high, which is why I like to put them in their own space. This way, I can monitor the sound that the mics are hearing, and move them around accordingly, to get the tone I want.

As far as mics go, I'll normally use a 57, or a 609, on axis, with a large diaphragm condenser off axis. The on axis mic tends to sound very mid focused:

1. because it's on axis, and
2. because it's a dynamic,

as opposed to the condenser mic, which sounds comparatively scooped in the midrange, but has more top and bottom. So these two sounds kind of represent the opposite ends of the midrange sonic spectrum, as far guitar tone goes. I'll normally blend these two mics to create the tone I want. If I had to use just one mic, It'd be a 57, and I'd move it around to get the sound I wanted
As far as effects go, I'll normally use any effects straight into the front of the amp, rather than add them later in mix-down. I feel that sounds more convincing. I'm a fan of analog stompbox type effects, as opposed to multi fx units, which seem to rob some of the guitar's natural tone, so I'll rarely use multi fx. Certain time based effects I will add later, but everything else goes into the front of the amp.

If I'm not using an amp, for whatever reason, I'll usually use a pod, or a tonelab in it's place, but in the same way that I'd use a real amp. Using software plugins can be cool too. I've got some really cool sounds using DI'd guitar, and re-amping through a plugins.