While I am not disagreeing with the general point of the original post in this thread, there are some inaccuracies there and in a reply or two. My point is not anti-Kenny Williams either.
Matt Guerrier has gotten Major League time with the Twins and will probably continue to do so. Was it a big blow to lose him? No, but at the same time, he had significant value at the time. While the trade worked out for the Sox very well, I wouldn't discount him as giving up nothing. Losing players like him (and not only him) hurt the depth of your farm system. Good depth can allow other players to develop at the proper pace and not be rushed. Even though all players won't make the Majors, having depth can actually help other players develop properly and succeed.
You can say the same for Jon Rauch and Gary Majewski.
The Sox gave up a lot in the first Carl Everett trade. Frankie Francisco will continue to pitch in the big leagues, last year's incident notwithstanding. Both Anthony Webster and Josh Rupe had nice years last year despite each losing some time to injury and are on good developmental pace. Webster, still only 21, hit .287 with 35 extra base hits, scored 66 runs and stole 20 bases in only 99 games last year. Look for him to possibly break out this year and jump right back onto the prospect lists.
Rupe will play this year at 22 and should start in AA, where he finished last year. He battled injuries last year, yet still he dominated in High A coming off the injury and more than held his own in AA. He is still very much a legitimate prospect.
The reason the Sox system was considered "so far down" is that those trades really ate up the depth at the top of the farm system and the talent was at the lower levels. Many top lower level prospects never pan out, so unless they are the cream of the crop, they are not weighed as heavily when rating a farm system against other clubs who do have better talent at the top.
The Sox system "jumped" in the ratings, because they had a very successful year with lower level prospects suceeding at higher levels. Brian Anderson finished the year in AA and had some success before nagging injuries made him tail off at the end. Ryan Sweeney, just a year out of HS, held his own in High A after skipping Low A. Brandon McCarthy, while he had put up excellent numbers, spent two seasons in rookie ball and had never done it for a full season, so he made a huge jump. Gio and Francisco Hernandez were not on the radar. Chris Young was still raw and coming off of two years in rookie ball.
It would be very nice for all of the aforementioned parties to continue on an upward track along with some others, but the odds aren't in favor of that. I think it is certainly legit to say that the Sox system made a big jump last year, but I would also caution at rating it amongst the top 5 in the game.