The so many problems exsits in my bike!

I really can't help you with the clicking noise, but it is not uncommon for a chain under load to either not shift or to over shift and come off the chain ring. This tends to happen more often with Shimano components but it can happen with any manufacturer's drivetrain. The only way to correct this is to ease up on your pedaling and let your momentum propel you while shifting so that you are not shifting under load.

After all that you have tried to do to eliminate your clicking, it may be time to bite the bullet and take your bike to your LBS and let them take a crack at fixing it.

I doubt that it is but if the crank is actually hitting the frame then you should be able to tell (the paint should be at least scratched or marred at that point).

Moving spokes make a distinctive noise (pluck one to hear the same tone). You'd know immediately if it were them. Greasing them (except in the thread when building wheels) is not a good idea as it is unnecessary and just attracts dirt. If the spokes are moving against one another then the wheel was not built properly.
Eyelets usually will not click in time with pedal revolutions, they will do so in time with wheel revolutions.

If it is not happening in the rain then water is lubricating the two mating metal surfaces responsible. Since water can get in almost anywhere this doesn't really do much to eliminate too many potential causes.

If it only happens when standing or both when seated and standing then forget about anything to do with the saddle.
The most likely candidates (after what you have already done) then would be:
Crank bolts (if you have a taper/octalink BB)
Pedal threads (grease and tighten)
Pedal/Cleat/Shoe interface
Handle Bar clamp (usually just tighten)
Stem to steerer clamp (usually just tighten)
Headset (probably requires a bit of grease - take it to the shop for that)
Dropouts (make sure quick releases are tight)

A little grease in the BB threads should be more than enough to prevent it from creaking. Plumber's tape is definitely overkill.

If it only happens when in the saddle then it must be the saddle, saddle clamp or seatpost clamp. You don't reef hard enough on the bars when seated to bother with that usually.