How you might avoid loading jQuery twice (until it's a prefix)

yepnopehelper.js

// If you always need jQuery regardless
yepnope([
  {
    load: 'jquery.js'
  },
  {
    test: Modernizr.something,
    nope: 's1.js',
    complete: function () {
      $('*').s1();
    }
  },
  {
    test: Modernizr.somethingElse,
    nope: 's2.js',
    complete: function () {
      $('*').s2();
    }
]);

// If you can avoid loading jQuery altogether if both fail...

yepnope([
  {
    test: Modernizr.something && Modernizr.somethingElse,
    nope: 'jquery.js'
  },
  {
    test: Modernizr.something,
    nope: 's1.js',
    complete: function () {
      $('*').s1();
    }
  },
  {
    test: Modernizr.somethingElse,
    nope: 's2.js',
    complete: function () {
      $('*').s2();
    }
]);

// But soon, we'll do a 'once' prefix, and you can do it like you tried before

// First include the prefix (concatenate it into the yepnope.js file)
yepnope([
  {
    test: Modernizr.something,
    nope: ['once!jquery.js', 's1.js'],
    complete: function () {
      $('*').s1();
    }
  },
  {
    test: Modernizr.somethingElse,
    nope: [ 'once!jquery.js', 's2.js'],
    complete: function () {
      $('*').s2();
    }
]);

// Or if you live more dangerously, we could also have a 'once' filter (which would just look for the same url twice, and skip it if it happens again)

// First include the yepnope once filter (concatenate it into the yepnope.js file)
yepnope([
  {
    test: Modernizr.something,
    nope: ['jquery.js', 's1.js'],
    complete: function () {
      $('*').s1();
    }
  },
  {
    test: Modernizr.somethingElse,
    nope: [ 'jquery.js', 's2.js'],
    complete: function () {
      $('*').s2();
    }
]);

I think my only aversion to adding in the duplication stuff is filesize. I was trying to keep only the most common cases supported by default, and then wanted to build a robust set of additions so the loader could work the way you want it. However, I could probably do this one thing with relatively little amount of code. I'll look into it.