Any of them fit. They bolt directly to the transmissions of the Fiero. I recommend the 4T65eHD automatic behind the 3800 Series II/III engines. The GETRAG if you are doing a manual install. The Isuzu will work if you do not plan to drag race it.
89-95 are series one and this covers natural aspirated and supercharged. Not recommended unless you are on a strict budget and are willing to only save about $1000 instead of doing the SuperCharged version.
96-03 These are the WOW factor engines. Series II SuperCharged engines. They come from Grand Prix, Regal, Park Avenue, Road Master, and a couple others.
04-06 I know the Monte Carlo and Impala have the Series II SuperCharged for 04, and the rumor is that this engine is being used until 06 with Chevrolet.
04-06 The Series III SuperCharged came out in the Pontiac Grand Prix. Rumor is that the Grand Prix will get the V8 4.8 or 5.3 as an 06 model.
*Note: I know the 95-96 year models were transition years for the Series I and Series II. You can find some Series II's in 95. I personally use 99+ only engines with 30k or less on my turnkey 3800SC installs.