You'd think the crowds of NYC would rule out this sort of petty arts larceny (petty artsceny?) but it turns out that the carelessness exhibited in so many multiplexes—which, incidentally, also serves as a justification for this behavior; I think of it as poor management tax—makes for the perfect two-for-one experience. With a few well-placed sneaks, you can bring your average ticket price down to early-aughts levels!
General tips: Don't make your free one something that's likely to be sold out; that's just rude and ruins it for the rest of us. Don't get freaked out by the employees; unless they have been specifically assigned to check tickets, they will probably be concerned with other stuff, such as selling popcorn and/or sweeping up popcorn that they sold two hours ago. Remember how hard it was to get in touch with someone to tell them when the movie was playing backwards and out of focus? It's even harder to get someone to come up to you if you act like you're supposed to be there.
Timing: Generally, it's best to slip into the second theater during the middle of the Twenty, or whatever they call those pre-show ad packages. This assures you will be early enough not to disturb anyone, but late enough to not feel bad about taking an open seat. Plan your showtimes so that you're not forced to kill an hour between movies (or watch the Twenty repeatedly). Probably no one at the theater will care if you're milling around for awhile, but, say, sitting somewhere and reading will raise a flag—so unless they have a claw machine, you're gonna get bored with too much time between. Alternately: get really, really good at the claw machine.
AMC Empire 25: If you're going to sneak around in Times Square, this is a better target than the neighboring Regal: more screens, better variety of movies, and only one point of ticket-ripping. Ushers will herd you towards the exits when you leave, but as long as your second movie is a lower floor than your first, you should be good to go—just hop off the escalator. The automated ticket kiosks will provide helpful information about what movie is playing in which room. (If your second movie is higher up, it's still doable; just be a bit more stealthy about using the restrooms or concession stands as cover for your movement.)
AMC-Loews at 34th St.: More easy pickings, thanks to a middle bathrooms-only floor that actually encourages you to travel between levels, but both the sound and the crowds here can get a little mangy.
Regal Union Square 14: Probably the easiest sneak in Manhattan; to toggle between floors, just use the stairs in the back rather than the escalators (misdirection!). Only problem: many of the theaters are small, so make sure your sneakquel isn't enjoying an unexpectedly boisterous fifth weekend at the box office. Oh, and their claw machine is broken.
Regal Court Street: One of the more sneakable multiplexes in Brooklyn—but you may lose all hope while ascending and/or descending the dozens of escalators it takes to get in and out. AMC-Loews Lincoln Square, Kips Bay, Village: Avoid 'em. The multiple-floor systems make these places trickier to navigate: often the releases waning in popularity that make perfect second halves of double features are sequestered downstairs, behind a separate ticket-taker at Lincoln and Kips. Also, you probably shouldn't try it at the Angelika unless you're free on weekday afternoons. Not because I care about giving the Angelika money, but because that place can be a cluster-cuss even if you're on the up and up.
If You Get Caught: Just go with the old-person defense: act confused, a little irritated, and a little sad. Note: this has never happened to me, so I don't know how sound this advice is. If you feel like you need to drop a smoke bomb and disappear into the haze, go for it.