Best Format For Audio Loop Samples To Use with SONAR (Acid, Apple Loops, RMX or REX)?

Not an easy question to answer because it depends on the type of material. Here's an excerpt from an article I wrote in the January 2014 issue of Keyboard magazine: 
 
There are three main stretchable loop types. REX files detect the transients in a piece of audio, create “slices” at these transients, and associate each slice with a MIDI note. These MIDI notes form a sequence that plays the slices sequentially; so speeding up the sequence speeds up the rate at which the slices play back, thus increasing the tempo. The reverse happens when you slow down the sequence. REX files are ideal for percussive tracks, particularly if they aren’t melodic and don’t have sustained sounds (e.g., cymbal crashes). Single-note lines, like bass, sometimes stretch well, too. REX files can have excellent sound quality, as slicing the audio doesn’t change the fidelity, only the duration; however, slowing down can leave gaps between the slices that may or may not be problematic. Changing a REX file’s pitch applies DSP; the quality of the results depends mostly on the transposition amount.
 
The Acidized and Apple Loops formats also detect transients but instead of slicing the audio physically, they employ DSP to lengthen these sections to slow down tempo (or shorten them to speed up). To avoid discontinuities in the transitions between sections, Acidized and Apple Loops files apply crossfading to smooth the sound. The files don’t always work as well with percussive material as the REX format, but often do a superior job with sustained sounds or sounds where you need to transpose pitch.
 
Bottom line for me is REX for percussive sounds with distinct hits, Acidized for anything else. But read the article for hints on how to make your own "faux" REX files in SONAR.

Boydie
Is there a format that is easier to convert to the other if I needed it
 
eg - if I went for the REX files could I convert these to a WAV file within SONAR and then do any transposing?

 
Yes, but you can do that with Acidized files as well. The main thing is you will need to convert to a WAV file to transpose, and converting will lock any issues in place.
 

Would that give me the best of both worlds? - ie buy the REX files, play with the song to get the tempo right, convert REX to WAV and then transpose?

No, because REX files aren't always the ideal choice, e.g., for pads. If I could choose only one or the other, I would choose Acidized files because I can edit them in SONAR. REX files can only be edited in ReCycle. Not to diss anyone, but many commercial libraries do lazy acidization or "rexifying." Either one takes a lot of effort to create a file that will stretch well and sound decent over a wide range. Where REX files have the edge is percussive loops with strong individual hits, but Acidized files are almost as good if you don't need to slow them down too much.
 
Either one speeds up better than slows down.

My process for deciding which format is ideal is simple:  If I am planning on chopping it up (breakbeats, percussive bass lines and other things i would rearrange), REX all the way. It's a real timesaver. Otherwise I go acidized.