I think You're My Best Friend is a great Queen song and while John Deacon didn't write as many songs as the other band members I like his work. I don't have anything against bands and band members exploring soul/R&B/funk (e.g. Mick Jones of The Clash and later Big Audio Dymamite) but sometimes it doesn't work out whether from an artistic point of view or the fans not accepting it or both.
Queen's Jazz IMO is a very under appreciated album. Coincidentally I've been listening to it this week and thinking about writing a review on it!
The version of REO's You Get What You Play For that is on CD, from what I've read and understand does not sound like a good package. In attempting to squeeze four sides of a long two vinyl record set onto one CD they left off a couple tracks (Gary's Guitar Solo, Little Queenie). I think a lot of people are particularly disappointed by Gary's Guitar Solo being left out. Personally I think "Side 3" of the original vinyl version (Flying Turkey Trot, Gary's Guitar Solo, 157 Riverside Ave., Ridin' The Storm Out) kicks butt and I narrowly prefer it to the live recordings on "Side 3" of A Decade of Rock and Roll.
I guess another "unfavorite" that can be added to the list in this thread due to poor execution would be the initial releases on CD of old ZZ Top albums such as Tres Hombres and Rio Grande Mud.
As an afterthought I'll add Metallica's St. Anger. It is horrible and I do not even include it in my "collection" for completist purposes!