Just tested it with MegaMan X - pretty much 1:1. Zero lag.
I retested on a newer version. You're right, they seem to have corrected the lag within the past year or so since I tried an older version. Happy to see that it seems to be just as responsive as Super GNES now. So yup, SNES9x EX wins easily now. Glad the author seems to have ironed out the kinks. Plays fantastically even with my old Samsung Fascinate coupled with a Moga Hero. I even tested the increased difficulty romhack Mario RPG Armageddon and had no trouble with the precise timed button presses required in battle (I mention this hack here because the timed hits were altered to require far more precise timing than the original game, i've found it a rather good way to gauge input latency). I'm also plowing through action heavy games like Megaman X, DKC Trilogy, Mario World and Yoshi's Island as if I were playing on a real SNES (and the only mistakes i've made have been my own fault and not because of lag).
For those who don't have powerful enough phones/tablets to run EX+, you can still get the older version from Robert Broglia's website. It might not be as compatible as the plus version but it's still a step up from Super GNES in terms of compatibility and accuracy. Google seems to have removed the emulator, but he still keeps it up to date for download on his own site-
http://www.explusalpha.com/home/snes9x-ex/downloads
Robert Broglia's other .emu emulators are also fantastic. I generally use them for all retro based systems- MD.emu, PCE.emu, NES.emu, GBC.emu etc. And if you've again got a device that can handle it, GBA.emu is about as good as it gets for Gameboy Advance, I believe it's based on VBA-M and shares that emulator's compatibility. It's unfortunately too much for my old Fascinate to handle. So until I get a better device i'm stuck using My Boy!, it runs perfectly and is still infinitely preferable to Gameboid at least (I haven't run into any graphical or sound glitches, or missing mosaic effects for instance that I found common on Gameboid). There are some minor rare glitches, i've found Rayman 3 to crash on some of the mode7 style race course for instance. And it actually runs some games TOO well, for instance it Doom 1 and 2 actually run far smoother than on the original GBA (i'm not complaining about this because it's actually pretty cool in practice, but it is probably a sign of underlying inaccuracies that is likely causing other things to break under the hood). But it does seem suitable for my purposes until I can opt for a superior option.
N64 using mupen64plus AE was very mixed, how well it runs depends on the game (and I have to keep internal resolution at the N64's native, increasing it seems to kill performance by a lot). Less hardware intensive games like Mario 64 and Kirby 64 run fairly well with some minor frameskipping (though some texture flickering in Kirby). Banjo Kazooie also ran ok. But more intensive games were too slow. Paper Mario requires a fair amount of frameskip to run at full speed, and frameskip causes flickering in this game (even with the glide plugin). Non-glide plugins are faster but much glitchier (same rule applies to N64 emulators on PC). Banjo Tooie is much too choppy for my tastes. Conker I recall being slow as molasses (no surprise given that it took quite a while for even PC's to run it relatively glitch free at full speed). Donkey Kong 64 I was initially surprised ran incredibly well, though I soon discovered that there are severe game-breaking collision detection issues. Most of the surrounding level geometry isn't solid on the sides and you can simply walk through the walls and get stuck where you're not supposed to be (even the first training area doesn't appear to be passable, I got stuck trying to throw barrels only to find they just rolled through the walls instead of breaking as they were supposed to). Still present in the latest version of the emulator. It's a damn shame because I was pleased to see how fast the game was. You can technically fix the issue by enabling interpreter in the settings, but it causes the game to run unplayable slow for me (again a more powerful device might help here, don't know).
I've also found that bluetooth pairing is somewhat unstable for me with mupen64plus ae. Doesn't seem to happen outside of this particular emulator, but numerous times i've had my wireless controllers disconnect on me when playing. I'm suspicious it's caused by my device being too old and not powerful enough to run this emulator ideally, as i've found it commonly disconnects whenever I run hardware intensive games or enable settings that cause slowdowns (enabling the interpreter in DK64 for instance caused it to disconnect, which also had the effect of causing cripplingly slow speed in the game and likely stressing the CPU). So I think it may be related to my phone just not being fast enough or possibly running out of memory. I've had it happen on two totally different controllers to rule out it being caused by the controller (iPega and Moga Hero) and having tried multiple different Android operating systems.