Public bug reported:

VirtualBox does not show up anywhere in Gnome-shell as an application.

Wine doesn't show up anywhere in Gnome-shell as an application.

Those are two of the more egregious examples. I can run them from the
command line. The .desktop entries clearly exist in
/usr/share/applications. I've verified and reverified all the .desktop
entries and checked them against the Gnome documentation to verify
everything is correct. Yet it simply refuses to load these apps. A dump
of the VirtualBox entry dumped below (even editted it to use absolute
path).Similar problems with Wine which was installed via Ubuntu software
so no reason for it to be rejected/disappear.

Ubuntu: 20.10
VirtualBox:   Installed: 6.1.16-dfsg-6~ubuntu1.20.10.1 (from ubuntu Groovy 
repository)
Wine:   Candidate: 5.0-3ubuntu1 (also from Groovy repository)

...so...all are pointing to the current repository (Groovy). I'm at a
loss here even how to fix it since I can't really "upgrade" or "fix" the
.desktop entry since nothing is wrong with those. They are just "ghosts"
as far as Gnome-shell is concerned.

[Desktop Entry]
Name=VirtualBox
GenericName=PC virtualization solution
Type=Application
Exec=/usr/bin/VirtualBox
TryExec=VirtualBox
Keywords=virtualization;
Keywords[de]=Virtualisierung;
Keywords[ru]=виртуализация;
MimeType=application/x-virtualbox-vbox;application/x-virtualbox-vbox-extpack;application/x-virtualbox-ovf;application/x-virtualbox-ova;
Icon=virtualbox
Categories=Emulator;System;Utility;
Actions=Manager;
Comment=Run several virtual systems on a single host computer
Comment[de]=Mehrere virtuelle Maschinen auf einem einzigen Rechner ausführen
Comment[it]=Esegui più macchine virtuali su un singolo computer
Comment[ko]=가상 머신
Comment[pl]=Uruchamianie wielu systemów wirtualnych na jednym komputerze 
gospodarza
Comment[ru]=Запуск нескольких виртуальных машин на одном компьютере
Comment[sv]=Kör flera virtuella system på en enda värddator

[Desktop Action Manager]
Exec=VirtualBox
Name=Open Oracle VM Manager
Name[de]=Oracle VM Manager öffnen

ProblemType: Bug
DistroRelease: Ubuntu 20.10
Package: gnome-shell 3.38.2-1ubuntu1~20.10.1
ProcVersionSignature: Ubuntu 5.8.0-41.46-generic 5.8.18
Uname: Linux 5.8.0-41-generic x86_64
ApportVersion: 2.20.11-0ubuntu50.5
Architecture: amd64
CasperMD5CheckResult: skip
CurrentDesktop: ubuntu:GNOME
Date: Wed Feb 10 08:01:17 2021
DisplayManager: gdm3
InstallationDate: Installed on 2019-08-07 (552 days ago)
InstallationMedia: Ubuntu 19.04 "Disco Dingo" - Release amd64 (20190416)
ProcEnviron:
 TERM=xterm-256color
 PATH=(custom, no user)
 XDG_RUNTIME_DIR=<set>
 LANG=en_US.UTF-8
 SHELL=/bin/bash
RebootRequiredPkgs:
 linux-image-5.8.0-43-generic
 linux-base
RelatedPackageVersions: mutter-common 3.38.2-1ubuntu1~20.10.1
SourcePackage: gnome-shell
UpgradeStatus: Upgraded to groovy on 2021-02-07 (3 days ago)

** Affects: gnome-shell (Ubuntu)
     Importance: Undecided
         Status: New


** Tags: amd64 apport-bug groovy third-party-packages wayland-session

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https://bugs.launchpad.net/bugs/1915270

Title:
  After upgrade to 20.10 multiple apps dropped

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