In cases where the album and single versions don't differ much (other than length), I'm fine with the album version.
However, when the hit single/radio version contains a completely different mix, different vocal, or where the album version lacks key elements (e.g.: the DJ Kool Kat "rap" on Paula Abdul's "Opposites Attract), I much prefer the single version (as that's what I remember from the radio/MTV).
Of course I'd imagine a station's focus can play into it as well. For example, a more "rock" focused station might use the original album version of "*** On Feel The Noize", while a more "pop" oriented one might substitute the shorter version with the edited guitar solo. A station that avoids rap might use the version of Michael Jackson's "Black Or White" with the rap section omitted.
There are cases where a few choice edits really tighten things up as well, Queen's "Fat Bottomed Girls", for example. (In that case the single edit is probably the most familiar, due to it's inclusion on "Queen's Greatest Hits").
...and there are some radio edit's that should never see the light of day, like the sanitized version of George Michael's "I Want Your Sex".......errr "Love" that some Top 40's were using. Thankfully, I bet that's "hard to find".