Well laptops and high power unfortunately don't mix very well to begin with, as you've found. That's why most people that do any serious work (what the system would consider serious, I mean) either use a desktop, or some high-dollar well-designed piece of machinery (like installing Windows on a Macbook Pro, that's a surprisingly-popular route for programmers, or going with some business-class Lenovo).
If you do intend to get a new one (cleaned the old one properly and it just has improper cooling design) then you might want to look for something with a lower clock speed and/or lower number of cores. Performance per clock is more important to keep the clock rate down to keep heat generation down, and if you don't need four cores (even modern emulators rarely use more than two) a dual-core should be easier on the cooling... and of course getting a machine designed well to begin with is going to be one of the biggest helps. A $900 Lenovo business laptop may have the same specs as a $600 Dell (for example), but most people learn eventually that the better design is just worth it.
Anyways since modern CPUs will underclock themselves when they get too hot (possibly a cause of your performance issues?), I suggest taking it somewhere that can take it apart and give it a deep cleaning just in case.
Well, I originally thought of getting a desktop, but that wouldn't work well for me since I like being able to hang out with my parents over the weekend (I like to bring a laptop so I can play games and use their infinitely more reliable internet connection, the one I have at my apartment complex sucks big time). But then I decided to get a laptop because of portability. Fortunately, despite the high temperatures, I've only seen it throttle the CPU once but never again, but didn't quite reach the TJ maximum of 100 Celsius. While I didn't want super high-end, I got something mid-range, originally priced at $1100, I managed to get a coupon reducing the price to $840, and considering the hardware it had, it was a good deal; Core i7 2670QM, 8 GB DDR3 SDRAM, 500 GB HDD, GT555M 1 GB GDDR5, I can run Skyrim pretty well on here I must admit.
Perhaps I'm simply being too paranoid to the point where I can't even enjoy using an emulator or PC game without having to habitually check the temperature every five minutes; I just might uninstall Core Temp so I'm not tempted to scrutinize the CPU. My GPU however, is perfectly fine an gets nowhere near 60 Celsius under load. I think I will call Lenovo tech support and see what I can do, as I doubt I can send the machine in to have it looked at. Maybe I should have done more research and I regret not doing so, because I should have gone with a CPU that can handle intensive programs like Dolphin/PCSX2 and so on, as I hear they generate less heat. Well, it could have been worse, I could have bought an overpriced Macbook Pro or Compaq. The other issue is that I'm not really in a position to purchase a new laptop (financial obligations, rent, school, etc) but a last resort if need be. I want this machine to last as long as possible, I really do and for the price I paid, it's pretty potent and gets the job done well.
The laptop cooler I have does help keep it safer levels and is made out of aluminum which helps with heat dissipation, but there might be better coolers out there that I could look at.
The one I have now is this:
http://www.amazon.com/Cooler-Master...e=UTF8&qid=1358466873&sr=8-4&keywords=notepal
But I might get this instead, that is, if it will help cooling more than it does now
http://www.amazon.com/Gaming-Laptop-Cooling-Turbine-SGA-4000-KKNF1/dp/B004G603E2/ref=sr_1_1?s=pc&ie=UTF8&qid=1358466932&sr=1-1&keywords=laptop cooler
Edit: Just found out those cooler fans are replaceable.