I recently purchased the Fender collection (1) for AmpliTube. 
 
I am slightly overwhelmed by the number of presets for lead and rhythm. I need to spend more time tweaking and playing around, but does anyone have any factory presets they regularly use as "go to's"? Or, any presets you've made yourself that you would like to share? 

I don't really use the presets, but my favourite (real) amp is the Fender Deluxe Reverb.  So I'll usually just go to that stock setup and change the amp knobs to what suits the song.  Sometimes the Fender Twin with the same game plan.  I don't usually change the cabinet or recording room settings.
 
My suggestion would be to Google a song with a guitar sound you like, and try to find what amp they've used.  There are enough music geeks online that detail this stuff, so it's usually not hard to find.  Then mimic that setup in Amplitube as best you can, and there's your foundation.  Then tweak to taste.

Marshall, I have gone through a lot of the presets, but not all of them. It gave me a good idea of what the plugin sounds like. But instead of spending time with presets, I would suggest getting to know the amps.
 
Like Matt, I also mostly go to one amp, the Mesa Mk IV head and let the cab get chosen. That's the starting point. Use the Fender amp in place of the Boogie. Play for a few minutes listening for how it sounds. Now adjust a tone control a little from the default and play some more and see what differences you hear.  Keep on with this process for thirty minutes and you will begin to learn what the amp sounds like, and how to dial in what you're looking for. As you play, make sure you go up and down the neck also.
 
My favorite thing in the Fender collection is that Fender Triangle Chorus! That thing sounds great. Love it. 
 
I do have a few presets that I have but they most use the Boogie stuff.

I am not using any presets, but from the Fender 2 collection I use a 57 Bandmaster with a little compression in parallel with a 53 Bassman.

I also don't use much of the presets, but do like a "phat" tone. I use 2 different amps (on 2 separate tracks) and fine tune/tweaked each for taste.....has worked well for me.     

I agree about the Fender Twin, it's my default starting point. I got that Amplitube  deal too.
 
 

I think the key with the presets (which to me is a flaw) is that you have to make sure you are getting proper input levels within Amplitube for them to sound right. 

Deluxe Reverb is my favorite starting point.

Amplitube has too many options and almost none of them work for me. If I have to (or want to) use Amplitube for cleans I start with American Tube 1, increase master and reduce reverb. That gets me in the ballpark immediately. Hope that helps.

Hey, I like the Amplitube, but my workflow is different, maybe.
 
Lately, I record my bass track first, to a click track,
 
then I finagle a drum track,
 
then I record a guitar direct, with no sim at all, right now it is usually my American Strat into a focusrite interface.  Eventually I want to use my Gibson Firebrand 335 because it doesn't get much love lately.
 
Then I load an instance of Amplitube 4 into the effects bin, and cycle through different amps and presets.
 
 I never try to fit a song to an amp, I try to fit the amp to the song.  Does that make any sense.
 
I stumbled upon the Fender  Princeton in my last snert, it just fit the vibe, and the snert.
 
Life is great when you have so many options!  The Fender collection is FULL of them!
 
jqs