With regards to the spells you mention, I'd disallow them as they are for an underwater campaign. Most energy-based spells would be tricky underwater:
Melf's AA: Definitely out. The acid would be dilluted into uselessness the instant it is conjured.
Fireball (and any other firespell): Out. Fire and water just doesn't mix.
Cone of Cold: Hmmm... This could be interesting...
Lightning bolt: Could concievably have an effect similar to fireball; affecting a radius around what would normally be its point of origin.
This is just my 2 cents worth, of course. You could simply rule "It's magic; the spells work the same under water as they do above". Personally, I think it would be much more interesting to ban energy based damage spells, other than force effects and negative/positive energy spells. It would be a great opportunity to try out some of the less used spells. You could finally get to see a PC summon a fiendish shark!