First, there is no greater online resource for information on Jackson and Charvel guitars than the Jackson/Charvel Forum at wwwDOTjcfonlineDOTcom . If you have any question about identifying a particular model, this is the place to ask.

This Guide will attempt to briefly explain the major points that many Sellers simply do not know, and will hopefully assist them in accurately representing their Jackson guitar listings, and serve as a general guide for Buyers.

The most important thing to know is that the Fender buyout of Jackson did not reduce the quality of Jackson guitars. This is probably the biggest misconception concerning Jackson Guitars right now. I've owned USA Jackson guitars and basses from all eras, and can say with all honesty that Fender has not removed any of the quality that goes into Jackson guitars. If anything, they've improved it. Listings touting "Pre-Fender" as a selling point are yanking your chain.

Following a close second is the "USA/Import" confusion, and Jackson's Serial Number Chart.

1. Any Jackson that says "Professional" on the headstock is an import.
2. There are no known/verified "Prototypes" that were made in the USA and have "Professional" on the head.
3. Jackson's Serial Number Chart does not cover Imports.
4. Jackson serial numbers do not use 0's as "blanks" - if there's a 0, it's part of the number.
5. Import neckthrough models are serialized in the following manner: Jnnnnnn ; The letter "J" followed by 6 numbers, with the first number indicating the year of manufacture. J000123 means it was made in 1990, J100123 means it was made in 1991, etc etc. I haven't seen a recent neckthrough import, so they may be using 7 numbers by now. In any event, if the serial number is "J" followed by more than 5 numbers (including zeroes), it was not made in the USA. 
6. Neckthrough model serial numbers are always stamped on the end of the fretboard after the last fret. Some bolt-on models that did not have a neckplate are also stamped at the end of the fretboard.
7. USA-made Jackson guitars and basses do not always say "Made In U.S.A." on the head, but they never say "Professional", "Performer", or "Concept" on the head.

A brief history of the Jackson Professional line:

In late 1989/early 1990, the Jackson Professional line was started, and these were made with the same materials and construction quality as their USA counterparts. This is most noticeable in the neckthrough models, though the bolt-on models were also equal to their USA counterparts. Because of their high quality, the Japanese-made Professional models were outselling the USA models from 1990-1994, and in 1994 the Professional line was revised to further separate them from the USA models.
Sometime in 1997 or 98, Jackson removed the "Professional" marking from the headstocks, along with all other model-specific markings (Performer, Concept, etc etc).

UPDATED SECTION:

Concerning Jackson import models, specifically the neckthrough models, the serial numbers for models starting in 2000/2001 dropped the leading "J" from the serial number, and are now 7 numbers with no letter.

Concerning USA neckthrough models, starting in 1989/90, these models were given serial numbers that start with the letter "U". Many people misinterpret this as "UO" followed by 5 numbers. This is incorrect. The letter "U" was assigned to denote "USA-made" just as the letter "J" for the Japanese-made neckthrough models was to designate those models as "Made In Japan". So, a guitar with the serial number "U01234" is You-zero-one-two-three-four, not Oh-one-two-three-four.

USA-made Custom Shop Jackson guitars and basses do use the "J" serialization, but these will only have 4 numbers after the "J", and rarely will have 5 numbers.