Is there a way to make Skyrim not CTD from having too many .esps active at a time? I have so many mods and I don't want to remove them just because Skyrim can't handle them all. Can you increase/remove the limit at all or do I just have to choose wisely on what mods to remove?

Nope, the number of active data files (255) is a hard limit of the game engine that can only be increased by upping the engine to 64bit. If you are not at that number yet, then it means the engine is choking on the number of mods you have (Skyrim can't handle large numbers of mods being loaded like Oblivion could).

The limit is hard-coded at 256, however, you can only use 253 of those, since three are occupied by Skyrim.esm, Update.esm and the save file. Until Wrye Bash, or any other program, supports plugin merging, you're stuck at that limit.

Pretty sure it would only require Bethesda storing the load index in something larger than a byte.

Choose wisely, friend. The limit, EDIT: as stated above, is straight hard coded and can't be change.d

There are various ways to combine basic mods however. Get the texture combiner, and also learn to use the surprisingly Wryebash, which will merge most simple 'fix' mods and a few others into one patch, freeing up possibly 10-20 esps for you.

Otherwise, choose wisely.

AFAIK, this is an engine limitation, so no (Someone correct me if I am wrong). If you don't already use it, use Wrye Bash, as a Bashed Patch can merge some mods into it (those highlighted green), that way you can reduce your active mods somewhat. Also, post your load order, there are probably some mods you can remove because they are: (A) Outdated, (B ) they overlap or do the same thing, or (C ) are known to cause issues.

I'm pretty sure that the game would crumble anyway if one were to try installing 65,000+ mods (which is what 2 bytes would get you).

Or cause their CPU to melt.

65536 to be precise (65533 counting the required data files).

This engine can barely handle 50 mods being loaded, so I sincerely doubt it could ever handle that many.

Wrye bash still has functionality to merge some files, which can reduce the total number of active files. I have trouble believing there are currently 255 .esps you would have active without massive conflicts, unless you have an absurd amount of armor or something, or a mod that has ton of individual .esps.

Oh glob! Well here's my load order: *Deep breath*

1 Skyrim
2 Update
3 Unofficial Skyrim Patch
4 Weapon and Armor fixes - Hacks
5 Weapon and Armor fixes
6 LeatherBackpackBlack
7 LeatherBackpackBrown
8 LeatherBackpack
9 Dr_Bandolier
10 hothtrooper44_ArmorCompilation
11 Cloaks
12 ImmersiveArmorsNPCs
13 1nivWICCloaks
14 1nicWICSkyCloaksPatch
15 BandolierForNPCMasterFile
16 BandolierForNPCsWIC_V2
17 BandolierForNPCsCheaperBandoliers
18 BandolierForNPCsImmersiveArmorsPatch
19 SkyRealism - Mass and Materials
20 SkyRealism - Capacity and Carry Weight
21 SkyRealism - Encumbrance
22 SkyRealism - Detection Durations
23 SkyRealism - Simple Save System - 1 min
24 ACE Enchanting
25 ACE Melee
26 ACE Realistic Fighting
27 ACE Synergy
28 Speech Tree
29 Bodies Stay Longer (Extreme)
30 Bloodx10
31 DeadlySpellImpacts
32 DeadlySpellImpacts - Two Fire
33 Even Smaller Spell Light Radius- 65%
34 TRO_BasicNeeds
35 PersonalizedMusic_v4.0
36 PM_TempleMusic_v1.0
37 ScenicCarriages
38 SkyTEST-RealisticAnimals&Predators
39 Werewolves
40 smash locks and more
41 Starting Spell Choice
42 MountedCasting
43 iHUD
44 83Willows_101BUGS_V4_HighRes
45 Chesko_WearableLantern
46 Soul Pool Perk (I made this mod myself, it's on the Nexus )
47 Open Empty Containers
48 argonianraptor
49 Apocalypse - The Spell Package
50 MorePerksPerLevel
51 mmkhajiithair11
52 Morrowloot
53 Unique Booze Bottles Alternate Names Version
54 SeeYouSleepByMadmole
55 Open Cities Skyrim
56 UniqueWeaponsUnlimitedEnchants
57 Realistic Lighting
58 Better Dynamic Snow
59 Realistic Lighting Patcher
60 Blacksmithforge water fix
61 dD - Enhanced Blood Main
62 1stPerson_only_killcam
63 Added_Killmoves_All_Weapons+Last_Enemy_Limit_Removed
64 Skyrim Performance MOD 5min
65 Automatic Variants

Done *heavy breathing* That's all my active esp (excluding Skyrim and Update, they are esm)
Most of them are essential to my Skyrim experience, others are just awesome or great, little tweaks.
Now I just need to wait for the Magic Mod Man (MMM lol!) to come and save my Modded Skyrim?
I also have Dawnguard mods waiting for me once I get Dawnguard T_T
If you all think Wyre Bash can help, I'll attempt to learn how to use it again, tried once and failed horribly.

In anycase: INCREASE THE ENGINE LIMITATION, BETHESDA!!!!!!!!!! WE WANT ALL THE GREAT MODS!!!!

The engine limitation is not the issue here at all, you are still well below the limit. As I said before, this game cannot handle large numbers of mods being loaded at once like the previous ones could. The code is a lot more temperamental (and goes to show that this Gamebryo-centric engine really is on its last legs) than before, and as a result it is a lot easier to cause game-breaking problems.