Opinions:
Lustria--
It is the most complete of the fan created, GW supported settings. It has all the parts one needs to play a campaign, although GW never printed one scenario,
Dems My Gubbinz! (I have an e-copy if you are interested.)
The warbands are generally held to be more powerful than the Mordheim warbands, although I feel this is largely a matter of opinion. My group tends to restrict campaign warbands to the setting they were created for, so I don't have much experience with most of the warbands in any other setting except for the Tileans and Dark Elves, which we allow everywhere.
The Norse warband is the weakest of the lot and the Bordertown Burning version is much better balanced.
The Nemesis Crown version of the Forest Goblins is also far superior to the Lustrian version.
We use a combination of the Lustrian Amazons and the Mordheim Amazons as our Lustrian Amazons. (The Mordheim version eliminated all the skills and changed the special rules which eliminated all of the Lustrian flavor.)
I do not recommend using the Hazards written for Lustria. The rules are incomplete and make a mess of any attempt to play any scenario they are included in.
Khemri--
There are two versions of the Khemri rules: the Town Cryer and the original website. Both are annoyingly incomplete but in different ways. The Town Cryer version did not publish a key table that is required to play the campaign. You have to have the original version of the campaign in order to access the re-supply table. The Khemri version does not include an Exploration Table.
Warbands:
The original website's version of the warbands is stronger than the watered down versions published in TC. Of the original warbands I do not recommend the Hobgoblins or the Sorcerers. Nor do I recommend the Elemental lists from the original site. The Elemental list from TC is not OP. The TC warbands are so poorly written and so weak that they should only be played against each other or by a player deliberately trying to play a weak warband.
Special Rules:
The campaign setting featured two limits on trading and warband growth. Resupply and water resources. We stopped using the water rules after a couple of tries. My lads suck at record keeping. So they would either get totally confused about how much water they needed OR they would all look for ways to circumvent using the water rules at all. After one Undead warbands only campaign (except for my Arabs) we stopped using them.
Resupply means that you must roll on a table after a game to see where you can trade. You might be lost in the desert with NO water; you might find a merchant or nomads who will only have Rare 8 or lower items, charge 25% more and have no heroes for hire at all; or you might find a town or caravan which have no restrictions on trading and have ample water or free water (oasis). (I really like this idea. I use it in all wilderness campaigns now.)
Underground battles:
The original Khemri website had complicated rules for fighting underground. The TC#17 published a simpler version of those rules (also used in the Nemesis Crown). 17 also has a nice table of complex traps to use in dungeon battles.
Most Broken things:
The Monkey's Paw, the Lamp of the Djinn and the Flying Carpet.
We used a pick and choose method for deciding which rules to apply. We use most warbands from the original website, re-supply and some underground rules and the weather. From the TC we use the new miscellaneous equipment and the edited scenarios. We also use the chariot for the Tomb Guardians but make Drive Chariot a general skill rather than an academic one (which meant that a Mummy could not drive a chariot...)
Karag Azgal or Mousillon:
These settings were not completed in any sense by their creators. Mousillon has some interesting warbands, it also has the broken Blood Dragons. (I suggest that when the authors of a warband tell you its over powered that you take them at their word.) In general both settings are interesting, but would take a bunch of work to make them playable.
Relics of the Crusades--
This fan created setting is very well done. My review may be found here--
http://boringmordheimforum.forumieren.com/t140-supplement-relics-of-the-crusades