Here are a few things I changed on my personal site when I implemented them.

In jquery.fancybox.js I changed

From:

padding: 15,

To:

padding: 5,


From:

/*
	 *	Overlay helper
	 */

	F.helpers.overlay = {
		overlay: null,

		update: function () {
			var width, scrollWidth, offsetWidth;

			//Reset width/height so it will not mess
			this.overlay.width(0).height(0);

			if ($.browser.msie) {
				scrollWidth = Math.max(document.documentElement.scrollWidth, document.body.scrollWidth);
				offsetWidth = Math.max(document.documentElement.offsetWidth, document.body.offsetWidth);

				width = scrollWidth < offsetWidth ? W.width() : scrollWidth;

			} else {
				width = D.width();
			}

			this.overlay.width(width).height(D.height());
		},

		beforeShow: function (opts) {
			if (this.overlay) {
				return;
			}

			this.overlay = $('<div id="fancybox-overlay"></div>').css(opts.css || {
				background: 'black'
			}).appendTo('body');

			this.update();

			if (opts.closeClick) {
				this.overlay.bind('click.fb', F.close);
			}

			W.bind("resize.fb", $.proxy(this.update, this));

			this.overlay.fadeTo(opts.speedIn || "fast", opts.opacity || 1);
		},

		onUpdate: function () {
			//Update as content may change document dimensions
			this.update();
		},

		afterClose: function (opts) {
			if (this.overlay) {
				this.overlay.fadeOut(opts.speedOut || "fast", function () {
					$(this).remove();
				});
			}

			this.overlay = null;
		}
	};

To:

Completely removed that section as the transparent black didn't look right over my darker background on my site.

Other changes:

I changed the size of the prev, next and close buttons. Then changed the css file to to correct position.