For me (and others do it differently, much is how you "write" and plan your songs out):
1) Record scratch track demo - this may be guitar or piano only, or guitar + vocal. This is a guide track only. I first set an EZ drummer2 loop that feels about right as a general 'feel', find the right tempo, and use this as my 'click track' because I hate playing to a click!
2) I set markers based on the scratch track - verse 1, chorus 1, etc.
3) I then go back and decide if the tempo is alright the way it is throughout the song, or if it needs to be slowed or sped up at any points. If so, then I'll adjust the tempo where needed, mute the original scratch track and record another scratch track.
4) Next step depends on the song itself, because I do anything from simple 2-acoustic guitar songs, to piano ballads to full-out rock songs. But usually the next step is to record the rhythm instruments - guitars and keyboards.
5) Once I have those done, I have a better feel for what the song is shaping up to, and will start massaging the drum track - changing beats/loops up for different parts of the song, for example. I like to do this to give the bass something to work with. Next step is the bass guitar part.
6) Next for me are the vocals - lead vocal first with multiple takes, then backup vocals (if there are any).
7) Lead parts - guitars, keyboards. I'll lay down multiple takes most times.
8) "Leftovers" - synth pads to fill out the 'wall of sound' in choruses', percussion - shakers, tambourine.
9) Back to the drums. Time to get serious, check the drum sounds to see if they are still ok now that everything is tracked, start putting in the fills, changing timing and sounds on various parts. I'll do this later on, as the mix is getting "close". too.
10) I'm always "pre-mixing" as I track - setting relative volumes of previous tracks, so that the parts jive together.
11) Serious mixing starts - drum levels first, bass and rhythm instruments. Add reverb busses. Vocals and lead parts, comping when needed.
Hope this helps!