This will be a bit of an amalgamation of a few posts, mixed with things that I've come to find myself through playing. I couldn't find a post like this, so I thought I'd share. Special s/o to /u/0NightFury0, who in my opinion provided some of the best info but didn't get much recognition for their post.
Flora doesn't count.
If a creature has spawned and you haven't yet scanned it, it will appear as a red dot in your scan visor. Different genders are treated as different scans, but only one gender of a species is needed to 100% a planet. Previously scanned creatures (and genders) appear as green dots. Pesky birds? Shoot them down with your laser - you can always scan a dead animal.
Get used to spending a lot of time looking through your scanner; particularly on planets with infrequent fauna. If you're having trouble simply finding animals, send out a scanning pulse and enter scan mode - look for small white circles because this is where a creature (or a pack) will be. Walking is slow and running is impossible in scan mode. With a fully updated jetpack, you can use the punch-jump move, set off a scan, and enter visor mode to view a larger area much quicker while you're gliding above the ground.
HG has set it so that larger creatures (>~3 meters) spawn from further away than other fauna (and will also spawn when you're in your ship), so if you see a red or green dot that you think is somewhat far away, it's probably a big animal. This works for larger water creatures as well, but I'm not sure what the size threshold is (it seems to be >2 meters). Thus, if you see a white dot in the water via scan, it's probably a school of smaller fish or water-worms.
If you're like me, you have little trouble reaching that 90% mark, but the last one is much more difficult to find. The greatest hint is to check the discoveries page and see which position in the the list is missing, because there's an order to how the creatures are displayed.
Ground (including hovering, I think) > Air (includes flying fish) > Caves > Water
| L | R |
|---|---|
| Ground (aggressive) | Ground |
| Ground | Air (aggressive) |
| Air | Cave (aggressive) |
| Cave | Water (aggressive) |
| Water | Water |
It usually isn't too difficult to find a flying creature (flying fish are particularly common spawns), however, I've found the most difficult scan to be a wedge after the first bird I've found. That could mean that cave creatures are difficult spawns, but in my experience if there is a cave creature, it is very common in caves. Maybe a bug? In any case, I usually move on if this is last on my last.
When there are more than 14 (the max listed on the discoveries page) species, the game has trouble recognizing 100% completion, even though the blue box in the bottom right corner will acknowledge 100% completion after you've scanned the last critter.
On occasion your game may default to a 100% completion mark even if you haven't found all species. This happens sometimes when leaving the planet, infrequently when closing the game and returning, and I believe every time you leave a system and come back. Not sure if a bug or intentional to push players to move on. You can't submit these "bugs" as completed towards the milestone, but you can submit planets with zero wildlife (albeit for no credits).
**After three (or so) pages in the discoveries journal, finds are no longer accessible. Hopefully HG fixes this in the future because the discovery is a large part of why I play this game and it would be a shame to be unable to go back and view your work.