This doesn't specifically cover custom bosses, but I see no reason that it couldn't be mentioned.
So, if you have something useful to add, please do. This topic will remain sticky, right up here at the top.

Table of Contents:
1:You can overlap tiles by pressing O
2:You can add flags to secret combos
3:Pushable blocks will be shown in ZC, but not ZQ.
4: Combo page tip.
5:Underwater effect
6:Use layers
7:Dungeon design tip
8:Darkness tip
9:Tile editor tips
10:Layers can have flags
11:Cycling Door tips
12:Ganon Death info
13:Movable pots
14:Regrowing Bushes
15:1.90 Freeform Dungeons
16:Faster combo scrolling
17:Mass comboing
18:Lockblock tips
19:Floor tile puzzles
20:One time cutscenes
21:Timed maps
22:Light Puzzle
23:Step->Next Hookshot tips
24:FFC curve tips
25: Dynamic undercombos
26:Room flags
27:Upgrading shops
28:Bottomless pits
29:Guidedmissiles
30:Sidequests
31:Locked doors in freeform dungeons
32:Selective secret triggers
33:Shop tricks
34:Sword triggered statues
35:Cycling tile warps
36:Explosion generator