Low undergraduate GPA. Strong research profile. Any chances of getting into the likes of MIT, Caltech, etc? I am a final year undergraduate student of Mechanical Engineering from Nepal. I plan to do master's in aerospace engineering (propulsion systems, to be specific) at a prestigious university in the US. With virtually zero scope for aerospace engineering research in our country and little to no guidance from experts, I have been involved in many research projects for years and have already got a number of papers published so far. I hope to add at least three more conference papers to my profile before I apply to any graduate school.
But the problem is that I am going to have a very low CGPA, anywhere between 2.4 - 2.7. I have heard that many schools don't bother to look at anything else in an application when they see a low GPA and reject it straightaway. Does that mean I have no chances at all? I have been working very hard to offset my low GPA and make my resume look better than those of most other applicants. 
MIT, for example, recommends a minimum of 3.2 as a guideline. What does that mean for me?
Please respond.
If a department doesn't say they have a minimum GPA, then there is certainly some chance of admission - many departments make it a point to review all applications in full and refuse to use individual cut scores for any element of the application. And yes, some departments use cut scores anyway so if you don't meet their (often unpublished) minimums your app gets tossed.

Is it worth applying? If you can spare the ~$100ish US dollars, sure - the worst case scenario is you don't get a yes, and you'll most likely get a nice generic rejection email telling you how many applications they had this year and they just can't take everyone who's great.

The more important point is that you have only mentioned a few of the world's most famous institutions on planet earth at this time in history. All of them receive many hundreds of applications, and some applicants with no obvious negative marks, letters of reference from leading professors at that institution, and a masters degree from another famous institution (sometimes even that same place) and/or a bachelor's from another famous place...still do not get accepted routinely. If you'll only be happy with the least likely outcome, you are most likely to be disappointed. So if it's potentially a good fit for you and you have the extra funds, you can certainly apply - but I don't think it's helpful or wise to make it Plan A.

I suggest you apply to the famous places just to satisfy that drive to do so, but dig deeper. Look for places with a more specific fit to you with 2-3 people who are doing work that excites you, look for places you'd have an awesome opportunity at even if the institution name isn't a Hollywood-shorthand for smartypants (as the Batman Lego movie says, "Harvard for cops", or in this case "Harvard for engineers"), and search for places that also offer a variety of expertise that you think is interesting even if it doesn't seem like a perfect fit at first (if you get in you might find on a visit that there is something that just blows you away you never thought about). 

The process has a serious random component, and there is no well-ordered universal ranking of students, faculty, programs, departments, or institutions - i.e., there is no true best-worst that everyone agrees on. You just need to find one "yes" that works for you and your goals. Don't talk yourself out of aiming high, but don't let other people's marketing get in the way of your long-term happiness. Be strategic, apply broadly, work hard, have back-up plans, and you'll be ok.