We will not be discussing getting more performance from the original 2.8 or Duke. Seriously, take a look at what you have. It is a 30 year old motor. It is most likely already on its last leg. If it runs good, then enjoy it for what it is. If it needs rebuilt, a swap is probably a better value. If you want to stay stock...then look elsewhere for advice.
So...let's look at what it takes to do a swap. Some swaps are easier than others. Some swaps are well documented, while some will force you to blaze new trails. These are the areas you need to consider when doing a swap. Any swap.
First things first...you have to decide what engine you want, and what transmission you will put with it. I will assume you are planning to stay with a transverse mount...if you are looking to do longitudinal, and still need to read this, then you are already in over your head. In general, your biggest limitation is size, but if you are choosing an engine that was originally a longitudinal mount, we have to consider the location of the axle in the Fiero. Many longitudinal engines put the starter on the passenger side, which puts it right in the way of where the axle needs to be...so if you pick one of those, you will have to find a way around that. Also consider the exhaust output...there are a couple engines (Mazda rotary, for example) that simply can't be used because the exhaust output would be directly into the axle. Most transverse designs will fit without too much trouble.
Some important factors to consider when deciding on an engine:
Mounts - It needs a minimum of 4 mounting points. The stock design uses a front and rear mount on the transmision, a single lower mount on the engine, and a "dogbone" that controls the rotation by bracing it to the trunk side wall. If you are using a stock Fiero transmission, then you can use the stock transmission mounts for two of those points (please consider that stock mounts are not solid mount....so you will want to either redo those to be solid mount, or use non-solid mounts for the other locations). A single lower engine mounting bracket is generally not difficult to make to attach to the factory mount, leaving us with designing a dogbone mount. This can be difficult because the alternator is in that location on many engines. Also, most engines were originally designed to be in the front, and the stock dogbone for those are on the wrong side of the engine for the Fiero. An alternative is to replace the dogbone and lower engine mount with two lower engine mounts that attach to the front and rear cradle crossmember...again, this would be a custom design. If you are not going with a normal Fiero transmission, then you will also have to design a front and rear transmission mount.
Attaching the engine to the transmission - If you are using an engine and transmission that were designed to go together, then this isn't an issue. If you are using anything not designed to be together, then we have to first get them to physically connect. The easiest method is to make sure the transmission bellhousing matches the bolt pattern of the engine (stock Fiero transmissions use the GM Metric pattern...most common swaps utilize engines with this pattern). If they have different patterns, you will need to make an adapter plate. V8 Archie makes one to adapt a SBC or LS motor to the 60 degree pattern...beyond that, you are looking at a custom made piece.
Clutch/Flywheel/Torque converter - Again, if the engine and tranny were designed for each other, this isn't a concern. If not, each situation is unique. Make sure you have a way of fitting the starter into this solution as well.
Slave cylinder (manual tranny) - The stock Fiero transmissions use an external slave cylinder that pushes on the clutch arm. If you use a transmission where it pulls on the clutch arm, you will have to find a way to adapt that. Otherwise, it is simply adapting the hydraulic fitting to the new system. You will also have to keep in mind the hydraulic volume of the master cylinder, and adjust things appropriately.
Shifter - Anything other than a factory Fiero transmission will need a custom design to shift the transmission. This has been worked out for the common transmission swaps...otherwise, it is up to you to figure out how to make it work.
Axles - Again, a Fiero transmission will require Fiero axles...other than that, you will have to build an axle that uses the Fiero outer, new tranny inner, and is the proper length. Again, the common swaps have been worked out and you can find a parts list. Sticking with a GM transmission can make it easier to build an axle out of readily availabe parts.
Fuel lines - The new engine needs to get gas, so you will need to reroute/adapt the fuel lines. Also make sure the fuel pump is capable of running the new engine.
Cooling - There are 4 cooling lines needed....two for the radiator, and two for the heater core (unless you have an 87-88 Fiero, then you just need one for the heater core). You will need to find a way to adapt the hoses between the Fiero and the new engine. The big areas to consider are the direction of flow (some engines are a reverse flow of others) and a method of filling it and removing air. Unlike a front engine car, a Fiero needs to have access to the cooling system from the rear as well as the radiator.
Throttle linkage - You need to find a way to make the gas pedal control the throttle body. It is most likely going to be a custom design.
Air intake - You must find a way to get filtered air to the new engine. Most transverse front engine designs aren't difficult to adapt to the stock V6 filter box...but will that flow enough for the new engine? That is up to you to decide, and to find a solution if not.
Accessories (alternator, water pump, AC compressor, ets) - Are you using the accessories that came with the engine? Will the fit in their factory locations? If not, you will need to make a custom mounting solution for them. Are you keeping AC? If so, you will need custom hoses (or use the Fiero AC compressor and worry about custom mounts/pully). Keep the belt routing in mind here. If you are doing a custom accessory solution, you will have to make sure all the pullies match.
Exhaust - Most swaps will require a custom built exhaust. At least with an original transverse design you can usually get away with stock manifolds (if you don't want to upgrade to headers).
ECM/wiring - This seems to cause the most trouble for people. Every situation is unique. Most people use the ECM that comes with the new engine, and build a wiring harness to adapt that to the Fiero...but pretty much any of them will need a custom tune. Obviously a carbed engine is going to be much simpler. Again, the common swaps have harness designs readily available...otherwise, you are on your own. Consider what accessories you are using in the planning for this. Most people use GM engines, but there is no reason you have to. Non GM wiring can be more difficult to mate to the rest of the car though.
Now...lets look at some of the common swaps and the pros/cons of them. What you choose is very personal, and I don't want to turn this into a fight about which one is best. They all have advantages and disadvantages.
3.4 - The Camaro/Firebird 3.4. This one is so simple that I think you would be a fool to rebuild a 2.8. Other than a couple minor details (like the starter mount needing to be drilled), it is a direct replacement of the 2.8 long block. It allows you to use the stock tranny, stock mounts, stock intake, stock cooling, stock accessories, stock fuel system, stock throttle linkage, and stock ECM/wiring. It might need a bit of tuning to get the most out of it. It looks stock, but gives you a little more HP and a stronger bottom end.
2.2 - I think the easiest one to swap into a 4 cyl (manual at least, maybe an auto would work) is the 2.2L from a mid 90s Cavelier/Sunfire. It gives you more HP, very lightweight, and can even take a little boost if you want to go that direction. It mounts to the Fiero transmission, or you can bring the transmission from the Cav/Sunfire. Fuel lines and cooling are in the same position as the Duke, making that simple (actually uses stock Duke cooling hoses). It would require an engine mount and dogbone solution...and of course the wiring.
3800/3800SC - This seems to be the most common. They give a nice boost in power, with almost unlimited potential. All portions of this swap are well documented. Most of the custom parts you need can be purchased rather than actually custom made. The negatives here are my opinion, and are not open to discussion. The engine is heavier than most people realize...most swaps top 3100 lbs in the car...and I haven't heard one yet that I think sounds good. But...this is also one of the cheapest ways to make a truly fast Fiero.
SBC/LSx - This is also pretty well documented...mostly because V8 Archie blazed the trail for us. His kits will take care of most of the custom areas...but it takes extra consideration if you want to attach them to an auto. But...his kits aren't cheap...and the results can be heavy (about the same weight as the 3800SC, or a bit more for an all iron swap). It can also cause problems on the passenger side frame rail...especially with the water pump.
LS4 - This one seems to be picking up popularity. It has many of the same issues as the normal LSx, but comes with a nice auto tranny. It can be difficult to mate to a manual because of the starter location (it is on the tranny side, not the engine side).
Caddy 4.9 - This is the easiest V8 swap. It is an aluminum block so it isn't very heavy. It mates up to either the standard Fiero tranny or the 4T60e auto very nicely. It is well documented. It is also pretty limited in output.
3400/3500 - This is picking up popularity too. It mates nicely to a standard Fiero tranny, or the auto that it comes with. They can use stock V6 engine mounts. They can be done with stock V6 accessories, which can allow the stock v6 dogbone mount. They give a reasonable stock power...and can handle some boost. It can sound stock (or close), but won't look stock. It is also possible to use a 3400 short block as an almost direct replacement for the 2.8 if you replace the pistons to boost the compression ratio.
3.4 DOHC - I really haven't studied this one...but it seems to have similar pros/cons to the 3400...but gives the fun of Dual Overhead Cams.
Now lets look at some common tranny options. I am only listing trannies that have a stock Fiero bolt pattern (GM Metric).
FWD Getrag 282/284 - These are pretty close to a direct swap once you get the Rodney Dickman adapters and adapt the clutch line for the hydraulic throwout bearing. They are also a little stronger than the Fiero getrag.
F23 - This uses the stock Fiero axles, and the clutch/flywheel is pretty well sorted out at this point. It requires custom mounts, custom shifting setup, hydraulic throwout bearing adapter, and a method of converting the VSS signal. It seems to be becoming the go-to tranny for higher hp swaps. It is also available with multipe gear ratios. Make sure you get the GM Metric bell housing though.
F40 - This is the 6 speed from the G6. The 2006 trannies are readily availabe as 0 mile crate trannies for cheap. It requires all the customizations of the F23, plus custom axles. The gear ratios are limited and many complain about them...but they seem to hold up to power well. The 2007+ version has a quicker 3rd thru 6th gear.
4t40/4t60 - The non E version seems to be a pretty good swap for the stock 3 speed auto. It adds an overdrive, but is still controlled by a TV/kickdown cable. It requires custom mounts and axles...but they are pretty well documented.
4T60e/4t65e/4t65eHD - These require custom mounts and axles, but they are pretty well documented. They also require a method for controlling them...but most people only use them with an engine/ecm that came with these trannies from the factory, so the control isn't much of an issue. They can also cause some fun with the VSS, but again, it is well documented.
I don't claim to know everything, and haven't actually done most of these swaps myself...so I am more than willing to listen to other's thoughts...but again, let's avoid the "this one is best" comments....especially the all famous "3800SC is the answer to everything" that seems to be so common.