If you clear every peg on the level then all of the holes at the bottom are worth 100,000 and not just one of them.

For levels where you need mega points use Warren and try to save your green pegs for near the end. One of the bonuses he gives you is Triple Points. If you can get that and land in the 100,000 point hole at the bottom you're quids in.

You can get 100,000 points if you use Jimmy Lightning and catch both balls in the bucket while in Multiball.

Don't bother with the Pyramid as it's fairly useless.