We are also going to assume you have recently up to date maintenance. So no 150,000 mile timing belts, no knocking, no overheating, no puking oil. No smoking. A few drips of oil here and there are acceptable (sometimes I think MR2 means "leaks oil" in Japanese).
The stock ignition system is really good on a 3SGTE. You will find lots of old articles about cap/rotor wear etc. Those were wrong. We routinely make over 700whp on basically stock ignition systems, and field tons of "help me" calls about malfunctioning aftermarket coil on plug systems. Coil on plug systems are available, but require stand alone EFI and additional hardware. That adds up to money that could be put to good use elsewhere.
ATS sells a full tune up kit here (for 91-92) or here (93+). The included NGK plugs are pre-gapped a little bit too big. They will work for stock applications just fine, but we suggest dropping the gap down to .028 inches. While you are changing the spark plugs you should take the extra time to do a compression test. This is a good basic indicator of piston/ring condition. You are looking for 140-185 psi of compression. And it's very important that they are all within 5% of each other. Compression testers are available at your local autoparts store for under $30.
Your car will be louder now. If you are not comfortable with a louder than stock car then sell it and go buy a hybrid. Removing breathing restrictions is fundamental to making power. There are some quiet exhausts occasionally available on the market, but everything will be at least slightly louder than stock.
Intake: You've got a few choices here. You can go with an Apexi bolt in open element air filter like here. They flow great and still filter well. Or you can make your own with parts off ebay. Be sure you have the skills and patience to make a bracket, otherwise your filter will beat itself to death on the fuel filler pipe, quickly develop a hole, and no longer filter. Filters from HKS, Blitz foam, and Greddy Airnex should be avoided.
What a cheap freebie? Take the stock air box base, cut or drill more openings, specifically on the front and outside sides. Remove the stock air bladder from the firewall and reinstall with a new genuine TOYOTA air filter. Be careful to leave enough base material that it can still be bolted down. This flows great, and filters as well as OEM.
Exhaust: The $199 Ebay dual muffler dual tip exhaust flows awesome. We have seen 800whp from these before. Seriously. The bad news is that they are LOUD, especially when combined with downpipes and larger aftermarket turbos. The Berk exhaust does not flow as well, but is much quieter. TCS occasionally offers two exhausts: a quiet SP style exhaust that looks like a 3" version of stock. This is my favorite. It's difficult to make it fit perfectly, but it is quiet and flows reasonably well. The other TCS is the 3.5" dual muffler, dual tip, it's beautiful and BOLD (read: loud).
Downpipes: I'll get to those later. An exhaust can be changed out in about 2 hours at home. A downpipe takes 2-3 times that amount of time. I will also note that adding performance exhaust parts like a downpipe or a 2.75" b-pipe in front of a stock muffler is dumb. There is almost no gain in power because you still have a big restriction at the end. ATS Throttle Body Inlet–hey, it's my page I can push my own products if I want–The 1991-1992 cars NEED this. It's a 4-5 horsepower gain. Want proof that it helps? Well the 1993-1995 cars have a redesigned throttle body inlet that mirrors ours.
You have three choices (for now) based on budget. There is almost ZERO natrual...