Hm, this is a tough question (for me anyway). But, alas, here is my choice:
1. Crono's Resurrection - Having Crono helps in just about any situation. Luminaire, need I say more?
2. Sun Stone - Simply put, you need to complete this sidequest before the Rainbow Shell one. (I think...)
3. Rainbow Shell - Easy enemies, a very simple sidequest. Plus, you get Rainbow equipment at the end, which will help immensely in later battles.
4. Cyrus' Ghost - Hm, this one isn't too difficult, so I'll place it here before Ozzie.
5. Ozzie's Fort - Fighting Flea and Slash again is simple, but Ozzie, Slash and Flea as a trio can be rather difficult, therefore I placed it here, after having received Rainbow equipment earlier.
6. Geno Dome - This takes a while, and is also the best place to level up, I believe. Just watch out for Mother Brain, though... It's rather difficult to defeat.
7. Fiona's Forest - I had the most trouble with this one, so I left it till last. Marle, Frog or Magus are absolute musts here, by the way, due to the monsters in the desert being weakened by Water/Ice. The boss at the end of this sidequest is annoying, too, giving little time to recover from attacks.
That's just the order I'd complete them. Not sure if that helps.