MLS Transfer Fees (Received)
1) This list is by no means complete. I'm sure the sales of Luis Hernandez and Ariel Graziani are up there. They were loaned out first, though (and I believe they got transfer fees out of it), so there really wasn't an announcement. Carlos Hermosillo's another one. Did they get a fee when he left? According to Soccer America, they had a "special arrangement" with Necaxa for his rights. Plus, there's probably a few smaller players I'm leaving out.
2) It's likely "a nominal fee of $50,000" was paid by Everton for Joe-Max Moore, because his contract wasn't up until the end of the calendar year 1999 and they wanted him to join the team right after the MLS season ended. The source for that is Robert Wagman and Soccertimes.
3) There can be several different numbers floating around the internet for a single transfer. There's two major reasons for that. First is the exchange rate. Most MLS transfers are to England, so it's common to see figures in both dollars and pounds. It can become confusing as the exchange rate changes. For example, Tim Howard was transferred in 2003. The fee was £2.3 million. It was originally reported in the US as $3.6 million. But in this Reuters article from March 2004, it's reported as $4.2 million. That's because the exchange rate changed from around 1.6 dollars per pound to around 1.8.
Second, incentives are tough to figure out for the fans. Stern John's transfer fee is a good example. $3 million is the price from the Washington Times article I used as the source. But I kept seeing $2.4 million as well. According to Soccertimes, it turns out that $2.4 million was guaranteed, while it could have been worth up to $6 million with all the bonuses. There's a pretty amusing story about all this. A few years ago John was on the verge of scoring 15 goals for Nottingham Forest in a single season, and therefore triggering a payment to MLS. The team was broke, so they decided to bench him just because of that and would sell him at a cut rate price to Birmingham. As for the accuracy of the $3 million fee, I read on Soccer America that John did fulfill one of the bonuses, so I guess it seems about right.
Come to think of it, wasn't part of Tim Howard's deal incentive-based? We may never know the exact amounts.
EDIT: Altidore's deal is a similar example, it's reported that it could be worth as much as $12 million.