Depending on your firmware there are different ways to do this:

Fail-Mail trick - for firmware(s) 3.00 - 3.52 Show / Hide

1) Send yourself an e-mail with the following support_uri as link:

email:send?attach=ur0:shell/db/app.db.

2) Open your E-mail App on the Vita, wait for the mail and click on the link

3) Now just type in your e-mail address again and send back this e-mail with the app.db file as attachment. You will notice the E-Mail app close itself, thats normal and supposed to happen! :)

4) Retrieve the dumped app.db file with your PC's e-mail client and just leave it on your desktop for now..

HENkaku - for firmware 3.60 Show / Hide

1) Open your browser, go to henkaku.xyz and install the Homebrew Enabler

2) Open molecularShell and press select to start the FTP server

3) Use FileZilla and navigate to ur0:shell/db/ and download the app.db file

Backup Editing - for ALL firmware(s) Show / Hide

1) Install CMA/QCMA if you haven't already and make a full backup of your Vita.

2) Find out your AID (PSN Accound ID). You can simply find it inside CMA's file structure once you backed up your system. PSVita/SYSTEM/xxxxxxxxxxxxxxxx/

3) Now visit http://cma.henkaku.xyz/, enter your AID there and copy the generated key.

4) Next up you'll need to download PSVIMGtools for your OS and extract it somewhere.

5) Now copy the .psvimg backup file from your CMA folder next to the just extracted psvimgtools.

6) Run the following code via terminal.

psvimg-extract -K [Key] [FileName].psvimg [Output-Dir]

7) You can now obtain your App.db file from /output/ur0_shell/db/app.db

To make use of our custom icons, backgrounds, startups and whatsoever, we would need to install them somewhere on the Vita first. Because its hard to maintain files via the mail trick, the easiest and best way is to create and use a PSP Savegame! This way we can easily manage, re-edit if needed and copy our resources via QCMA without any complicated tricks.

Download

Inside our Customization savegame we can now create subfolders for each of our bubbles and keep the name 'icon0.png' multiple times for example.

e.g: ux0:pspemu/PSP/SAVEDATA/CUSTOMIZATION/vhbl/icon0.png

1) On the PC we now start the SqliteBrowser, open our app.db file, go to Browse Data and select tbl_appinfo_icon from the dropdown menu.

2) Here are all your installed Vita, PSP, PS1 and system apps listed.

3) You can now rename your Bubbles by simply changing the title to whatever you want!

4) When you're done hit Write Changes, close the programm and continue with Step 3.

icon0.png - 128x128

Note: This VitaFTP sample icon.png can be found in the customization savegame from Step 2

1) On the PC we now start the SqliteBrowser, open our app.db file, go to Browse Data and select tbl_appinfo_icon from the dropdown menu.

2) Here are all your installed Vita, PSP, PS1 and system apps listed with their links to the original icon0.png files.

3) You can now change the iconPath to any custom icon0.png in your savegame

e.g: ux0:pspemu/PSP/SAVEDATA/CUSTOMIZATION/VitaFTP/icon0.png

Note: PSP and PS1 icons will automatically turn to fullsize!

4) When you're done hit Write Changes, close the programm and continue with Step 3.

bg0.png - 840x500 (can be bigger or smaller though)
startup.png - 280x158

Note: Compared to just changeing the Icon, modifying the background and startup / default_gate icon is a little bit more complicated. We basically have two choices to go with:

The first one would be to overwrite the original files temporary located in the ur0 partition (ur0:appmeta/TitleID/livearea/contents/) or alternatively change the link to use our customization savegame instead!

Since our custom png(s) would simply get deleted when rebuilding the database with option 1, we will use the savegame method here:

1) The first thing to do now is to create a new folder in our customizations savegame and put in our custom png(s)

(this vhbl png(s) are already available in the customization savegame from Step 2)

2) Transfer the savegame via QCMA to your Vita!

3) On the PC we now start the SqliteBrowser, open our app.db file, go to Browse Data and select tbl_appinfo from the dropdown menu.

4) Search for your BaseGame's TitleID and the key:2630610402

5) Change the value to the folder our png(s) are located in:

ux0:pspemu/PSP/SAVEDATA/CUSTOMIZATION/vhbl

6) Go once again to Browse Data and select tbl_livearea this time. Search for your titleID and change the org_path to the same link as well. (ux0:pspemu/PSP/SAVEDATA/CUSTOMIZATION/vhbl)

7) When you're done hit Write Changes, close the programm and continue with Step 3.

Note: When replacing a PSP startup.png it will be aligned differently!!

Here is a fix for that: (thanks to @Chris_Fandino)

pic0.png - 480x272

Note: This custom 'bootscreen' sample pic0.png can be found in the customization savegame from Step 2

1) Transfer the savegame via QCMA to your Vita!

2) On the PC we now start the SqliteBrowser, open our app.db file, go to Browse Data and select tbl_appinfo from the dropdown menu.

3) Hit New Record enter your games TitleID and add the key: 1729228973

Also set val to the path where your png is located in the savegame
ux0:pspemu/PSP/SAVEDATA/CUSTOMIZATION/PIC0.PNG

4) When you're done hit Write Changes, close the programm and continue with Step 3.

Note: The following steps will exemplarily install a single frame with small Icon + text functioning as weblink. See this as addon to the Option 3 steps..

This VHBL sample can be found in xml form in the customization savegame from Step 2

1) Transfer the savegame via QCMA to your Vita!

2) On the PC we now start the SqliteBrowser, open our app.db file, go to Browse Data and select tbl_livearea_frame from the dropdown menu.

3) Hit the New Record button and fill out the fields like this:

4) When you're done hit Write Changes, close the programm and continue with Step 3.

Note: See this as a mini-wiki on how the template.xml and frames work. I will just give some examples, explain some of the tags and the basics. Nothing special..

Basic structure of a template.xml with frames:

FYI: When 'Please wait' is displayed after you open a new bubble, the content of the template.xml will be written to the app.db

The style parameter in the livearea-tag lets you select the basic layout:

With the frame tag and the parameter id="frame1" you create a new frame.

This is how the settings frame works for example: (style="a1")

(target declares the frame to be a clickable link and can be a http://link or URI)

Note: You can always dump the template.xml of any installed game to learn from!
ur0:appmeta/TitleID/livearea/contents/template.xml

Fail-Mail trick - for firmware(s) 3.00 - 3.52 Show / Hide

If this is the first time you are going to use this Mail-Installer method,
please make sure to follow this tutorial on how to set everything up first!

1) The very first thing to do now is to simply rename the 'app.db' file to '#0' without any file-ending!

2) Now we are going to write a new e-mail with the #0-file as attachment and the path we want the file to be installed as Subject. Send it to your vita!

3) If everything did go right you should see a camera symbol. Touch it and DO NOT click OK on the appearing Error Message but simply close the e-mail app completely!

HENkaku - for firmware 3.60 Show / Hide

Backup Editing - for ALL firmware(s) Show / Hide

1) Run the following code via terminal.

psvimg-create -n [FileName] -K [Key] [Input-Dir] [Output-Dir]

2) Copy back both created files in your output directory back to your CMA System folder

/PSVita/SYSTEM/xxxxxxxxxxxxxxxx/

3) Update the QCMA Database or simply restart CMA to find the changed files.

4) And finally restore the backup back to your Vita

Restart your Vita and your changes should be applied! Done!