Aug said: just about everyone uses 11's.
Actually, I set my action pretty low, especially compared to what I set it to in the days I used a custom set (at one time I used 014,024,034,044,046, and 060 on my 25.5" scale Kramer). I had basically a custom 014 gauge set, and I had buzz even when the action was set right, but you did not hear it through the amplifier. That's the criteria I use when setting guitars up is that some buzz is allowable, as long as it does not translate through the amplifier.
Also, going from heavier to lighter strings can affect the tension on the neck of the guitar. When I went from 012's on the Jaguar (what it came with) to 009's I had to lighten the truss rod nut about a 10th of a turn to get it just right.
I've found the heavier the strings, your sustain will drop just a little because it takes more energy to keep the string vibrating, but not as much as one would think because the added weight adds inertia to the string. The big part of it later onn was that I was using high gain and doing lots of fancy smancy techniques that were easier on lighter strings, so I went down to 11's and then 9's.
Basically, from my experience.....
Heavy strings take just a hair of sustain away, have a thicker tone, but at the cost of some clarity (hence why you almost never see a Les Paul or metal guitar with 14K buckers with super heavy strings, they are not as clear or punchy as a single coil guitar is by nature). The advantage is they provide warmth to more trebly guitars, build finger strength, and take away some of the buzziness in certain distortion sounds.
A good example of this was when I got the Jaguar I have, and it shipped with D'addario 012's (as I could tell from the ball ends on the strings), it sounded a little thicker, less top end and mids, and a little less punchy, a hair less sustain, but those strings paired with that ABR TOM bridge were not goin' nowhere that's for sure. I once also put 013 gauge flatwounds on the Jag-Stang, that was a huge mistake, my tone was very muffled and lacked lots of definition due to the bassy strings and active pickups, I prefer to use 009-040 strings on that one.
Light strings, on the other hand, have long sustain, and are easy to press down, and put less stress on the guitar as there is less tension (hence why most offset people don't like em' from what I hear, as they really move around on a Jaguar or Jazzmaster if you have a heavy pick attack and don't take what some deem a ridiculous amount of time to tweak it). On some guitars, particularly those with low output pickups or very dense tonewoods in their construction they will sound rather thin and brittle. Tele's with 009's and bad EQ can sound pretty grating on the ears (I always back down the treble and mids when running the Tele, and sometimes for the Jaguar too).
When I can, I put Fender Bullet 009-040' nickel Plated steels on the Jag-Stang, and 009-042' Fender Bullet Stainless on the Jaguar. The nickels are more trebly and react well with my EMG pickups, but the Jaguar I use the darker sounding stainless winds to make the sound more "dark", and the heavier bottom E to make the string both stay in place and bring a touch more warmth to the bottom end.
