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In this tutorial I'm going to be using, and recommending, BlockBench, for your modelling.

If you don't have a texture pack set up already you can check out the group FAQ here on how to do it.

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MODEL

First Step, Open up blockbench.

In the drop down menu on your screen, you'll see many options. For this tutorial, we're going to be making a custom model for a mushroom in minecraft.



Since we're creating a custom block for a minecraft resource pack, we're going to select Java Block/Item



A new empty project file is going to open up with these settings. We're going to ignore all of these for the moment. For simple models you don't have to do any of the following since we'll be doing all of this later when we save.

Once you've confirmed this, you can navigate up to Edit and click Add Cube.




Now you have the basic starting point of your model.



Here are all your tools.

Modeling has been made easy by the program.
To make your shape bigger, double-click on the cube to enter the Transformation mode.
To go back to the movement tools, simply double-click on the cube again.



You can also use the right side panel in ELEMENT, under Position, to move the cubes in a more precise way.
Note the color squares correspond with the direction.



GREEN - Up/Down Movement
RED - North/South Movement
BLUE - East/West Movement

While modelling, also make note of where the N (north) face is. This will help you keep track of the front of the model.

Using the BLUE Movement tools, we're stretching out the block in the example down below.



Play around with this to get comfortable moving around your cubes.

In the next example, I have switched between the Movement and Transformation tools to get my block the size I want it and where I want it.



Remember, this 16x16 plane in this program is the size of ONE minecraft block, surface wise.

If you need help to keep size in perspective, add another cube, make the size 16x16x16, and move it off to the side.
Just make sure you delete this guide when you later export your model into your texture pack.



If you go outside the plane while you model, that means in game your custom model will ALSO go outside the bounds.
This can be ok if that's what you're going for, you'll just have to remember to do Cull-facing later on so those pieces sticking out don't collide with others blocks and make a mess visually. (I'm not covering Culling in this tutorial)

With my first block in place, I'm going to again, go up into Edit and Add Cube. This is going to add a second element to my model. I'll use the Transformation and Movement tools until I have the shape I want in the place I want it.



Repeating this process, I will achieve the model I want.



You can also group up these blocks in the OUTLINER box on the right.

This will make it easier to move around a bunch of pieces at once, or if you have to manually edit the model .JSON down the road, as well as for keeping organized while you work.





You can rename the groups and the individual parts. Personally I don't mess with groups or renamed cubes in my personally projects, but if you plan on sharing your model with other people, it would help to label your parts!

TEXTURE

Now, you can do the textures in a different program, or right here in Blockbench.

First you'll have to figure out where the textures are going to be on your model. This is UV mapping.
In the above example, all the blocks have a different color. That's because Blockbench keeps track of each separate block to help you in texturing your model, and telling which separate cube is which.

In this image below, we have our Cubes in UV mode Box-UV. This keeps each individual cube's faces together, and there is a texture for each individual face on the mode. To save space and put all textures into one image, I usually do NOT use Box-UV and instead separate them out.



When you click the UV size, you will get a menu to change what mode is used.



How you want your UV is up to you. You can even use multiple pngs if you need to, do what's most comfortable. This is just a beginner tutorial.
I try to keep everything together in one file which means I tend to stick to Pre-face UV, which means I move around my UV pieces in one image, like below.




I use this method because a lot of faces will share the same texture, so there's no need to have duplicates faces when one will do the trick.

You will go under TEXTURES, and click Create Texture.



I am not using Rearrange UV because I will be doing that myself.
If you're using Box-UV method, you CAN and probably should use this method, as it will rearrange your UV like so



With Pre-face UV, how I figure out where each block is going to go is by switching back and forth between Edit and Paint modes.
In the right hand corner, you will see Edit, Paint, Display. Click on Paint.



Now you can paint on your model, and using the UV viewers, move around the faces in Edit.

I'll start with one cube at a time, moving around the pieces as I go.
Going back to TEXTURE, we'll create a new image, 32x32, with no rearrange UV.



Going into Paint, I'll use a color and bucket the face I want to see where it is on the UV map.



It might take some trial and error before you have the faces figured out, but that's ok. In the end, I'll have my flat colors down and mapped out in the UV editor the way I want them.



If you're doing a block that has the same sides, like this mushroom above, then you only need to texture one side and copy/paste the UV faces on the others.
This makes it so there's more space in the UV, and less work on you.

Once you get comfortable doing this, you can mash all these steps together, and do most of them at the same time. Like texturing as you move your UVs to save time.
For now, We'll keep to the steps.

You'll texture one side of your mushroom, like so.



Now, you'll click that same face you just textured and press CTRL + C, the copy shortcut.
This will copy the model and the face.



Now, you will click on the face you want the texture to go on, and press CTRL + V, the paste shortcut.

This will bring up a little window that asks if you want to paste the model or the texture. Click UV face, and it will paste the texture and the corresponding UV.




Now continue texturing.

My end result looks like this:




Before we save, make sure you set your particles.
If you do no do this, when you break this block in minecraft there will be pink/black textures. Like below



To do this, you'll Right-click on your texture, and select the 'Use for Particles' button.



Now, we're ready to export our model into our texture pack!

Click File, Export, and make sure you export this as an Item Model.



You'll rename this file to whatever the object is in minecraft. For this file, we'll be naming the file 'red_mushroom'

If you open up the .JAR in %appdata%/.minecraft/versions/[​YOURTEXTUREPACKVERSION] and go into minecraft/assets/models/blocks, you can search for the model you want and name your own file accordingly.
You may also import these models into blockbench and edit these instead of starting from scratch.
This will keep the original .JSON files, while letting you change the model, and you won't have to worry about doing particles.

Saving to Texture Pack

You've made, textured, and saved your model, now you have to move it to the right spot!

Navigate to your texturepack like so




Make sure it's in the right folder, assets/minecraft/models/block named right.

That should be it!

Load up minecraft. See your model, rejoice.
If minecraft is already open and your pack is already loaded up, just press f3 + T to reload the packs.
(Make sure you're using an unzipped pack if you're editing on the fly in minecraft. You will be able to see your changes in real time.)

Here's some extra tips/troubleshooting

IF YOU FORGOT TO SET PARTICLES WHEN SAVING YOUR MODEL, HAVE NO WORRIES!

You can always open your model back up in Blockbench and add the particles.

OR, you can open that model file with a text editor, like Notepad ++, and just add the line yourself.
I find myself doing this part often because I'm forgetful, but it's sometimes easier than doing it in the program.



Under "textures":, just add the line "particle": "block/[​WHATEVERMODELTHISIS]"

Make SURE you have commas in the correct place or the whole model will break.
For example, here I would add a comma to whatever lines are above "particle", while NOT putting a comma at the end of the line I added.This means everything in "textures" ends with "particle" and there's no more code to read.

I MADE A CUSTOM BLOCK, BUT IN-GAME IT'S HUGE IN MY HAND

This happens if you start a model from scratch. It's an easy fix.
You can go into 'Display' next to 'Paint' in Blockbench, but an even easier fix is just opening up the model file and setting a parent.
Sometimes a block needs to have a specific parent to work correctly.

Just on into the model file, on the very first line, set a parent block.
"parent": "minecraft:block/orientable", - is for blocks that can be placed orientable, like the furnace or a glazed terracotta block.
"parent": "minecraft:block/block", - in a general block. Looking in .JAR files for minecraft will tell you what your block is suppose to use.