If it's a '93 Tercel then your engine is a 1.5l, 12 valve, SOHC, engine code: 3E-E.
You have several choices for engine swaps.
First the easiest and cheapest swap is a Paseo engine. It's also a 1.5l, but it is a 16 valve DOHC, engine code: 5E-FE. It comes with 100hp@6400rpm, which is 20 more horsepower than the 3E-E, it responds better to modification, and it more realiable as it gets older. Because it's from the same engine family as your current engine, it is a direct bolt-in, and requires no physical modifications to get it in. This is probably the best swap for someone who will be doing this in their own garage or backyard or whatever. Plus, it's available here in Canada, which significantly reduces the cost over some of the other engines you could use.
Second, is a Starlet GT engine. It's a 1.3l, turbocharged, 16 valve, DOHC, engine code: 4E-FTE. In stock form it has 135hp. Alot of people are put off by the fact that this engine is so small, but don't be. It's small, light, and powerful, perfect for a car like a Tercel. With a few basic mods, it can easily reach 180hp. I've even heard of some as high as 300hp! Again, this engine is from the same family, so physically, it will bolt straight in. Although the installation is slightly more complicated due to all the turbo components. Unfortunately, it has never been officially sold in North America, so it must be bought from an engine importer, who like charge big bucks for engines such as this.
Third, is of course the 4A-GE 16v. 1.6l, 16 valve DOHC. Power ranges from 115hp up to 140hp depending on the year. It's a more difficult swap to do. It requires custom made engine mounts, because the engine is of a different family. Luckily the tranny will bolt on, but it requires 1 small modification to be made first. It has been done many times successfully. It was made popular in the Corolla GTS, and as such, there is huge aftermarket support for it. Because it is a North American engine, it can be found easily and is relatively cheap to buy.
Fourth, 4A-GE 20v. 1.6l, 20 valve, VVT, DOHC. Loads of really cool modern technology gets this engine up to 160hp in stock form. Installation is not significantly different than installing a 16 valve. But this engine must be imported, and can be very expensive.
These are the best swap candidates for a Tercel. Relatively speaking, they are not difficult or expensive to install. Theoretically speaking, there are other engines that would work (eg 3S-GTE), but the cost would so great that it would be cheaper to get a whole new car.
As for the tranny, you've got the 4-speed, which is much better than the auto, but could be improved by upgrading to the 5 speed. To do this, you can use the stock tranny from a Paseo, but it doesn't really have very good gear ratios. You could also take all the gears out of a 4A-GE tranny, and install them into the bellhousing you have now. This would give you much better gearing hence better performance. Though, I'm not sure if the 4-speed has the same housing as the 5-speed or not. That would have to be checked first. The best thing would be a Starlet GT gearbox. It bolts directly on, has the same ratios as a 4A-GE, and comes with a stock limited slip diff. If you end up performing a 4E-FTE swap, I'd suggest getting a complete front clip, that way it comes with the tranny as well.