Fishing in a Petrii Dish
* green gems add +x1 multi (x2, x3, x4, etc)
* purple gems add +x0.2 (?) multi (x1.2, x1.4, etc)
* shooting thick, white spine does more damage than thin white outer body
* more elaborate fish are worth more if kept intact
So, don't shoot fish directly in their center; it just breaks them apart reducing their value immensely.
Instead, find tail, shoot 5 times, wait. Shoot tail once every 5 seconds until dead. This minimizes structural damage (maximizing profit) while maximizing death damage (due to shots to the spine).
Best fish are large, intricate ones with green gems. However, even better is to nail a few small fish with green gems on the way down to easily bump your multiplier. Then go nail large fish below (preferably with purple gems).
Using this tactic, I got a x3.4 multi from two small, green-gemmed fish on my way down, then bagged $2000+ in the depths (including a $1200 fish!), and on surfacing earned almost $8000.
Then again, on free-play mode I bagged a $5000+ fish, and after surfacing with other fish, I netted almost $15k.
(I don't think you can beat regular mode. Which is sort of depressing, but also poignant at the same time. When you go into free play mode, you realize why, b/c they guy's a bad-ass.)