Many programs do both periodic and non-periodic calculations, so these are not categorized.
Many also do molecular dynamics, but for the more traditional dynamics programs, see the page on Molecular Dynamics and QM-MM Programs
ABINIT
ACE-Molecule
https://gitlab.com/aceteam.kaist/ACE-Molecule/-/wikis/home
Bagel
https://nubakery.org/quickstart/how_to_run_bagel.html
BerkeleyGW
BigDFT
http://bigdft.org/Wiki/index.php?title=BigDFT_manual
CASTEP
http://www.castep.org/CASTEP/Documentation
CCP5
http://www.ccp5.ac.uk/software
COLUMBUS
https://www.univie.ac.at/columbus/
CP2K
DALTON
http://forum.daltonprogram.org/
deMon2K
http://demon-software.com/public_html/index.html
DIRAC
http://www.diracprogram.org/doc/release-17/
DL_POLY
https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx
FHL-aims
https://aimsclub.fhi-berlin.mpg.de/
GAMESS
https://www.msg.chem.iastate.edu/gamess/
Gaussian
Lobster
http://schmeling.ac.rwth-aachen.de/cohp/index.php?menuID=6
MOLCAS
https://www.molcas.org/documentation/manual/node4.html
Molpro
Newton-X
https://www.univie.ac.at/newtonx/example.html
NWChem
Octopus
https://octopus-code.org/wiki/Main_Page
OpenMX
Orca
https://sites.google.com/site/orcainputlibrary/
Parsec
Q-Chem
https://manual.q-chem.com/5.2/
Quantum Espresso
https://www.quantum-espresso.org/
https://www.quantum-espresso.org/Doc/user_guide.pdf ;
https://www.quantum-espresso.org/resources/users-manual
RICC2
https://www.theochem.rub.de/~christof.haettig/webpage/researchtopics/ricc2_code.html
SCM Suites
Amsterdam Density Functional (ADF), part of SCM
https://www.scm.com/doc/ADF/Input/Input.html
SHARC
Siesta
Version 4.1-b3: https://siesta-project.github.io/bsc2017/siesta-4.1.pdf
Siesta 4.1-b4: https://launchpadlibrarian.net/396402638/siesta.pdf
Notes: the latest versions of Siesta (4.1-b4) includes the Transiesta manual with the program built into Siesta.
Tinker
https://dasher.wustl.edu/tinker/
Turbomole
VASP
https://cms.mpi.univie.ac.at/vasp/vasp/vasp.html
https://www.vasp.at/wiki/index.php/The_VASP_Manual
Notes: the VASP manual is entirely online, and available at several sources. Its vast and requires time to study the flags/keywords.