This doesn't include every single command in the game, since we would be here for a while. This only includes the commands I feel are important and everyone should know. If you want a more rugged, general place with ALL the commands for Source, this is a place with a good wealth of information: https://developer.valvesoftware.com/wiki/List_of_CS:S_Cvars

Even myself who has been hosting Counter-Strike: Source servers since I started playing doesn't know every useful command. If you want to recommend anything, feel free to comment on my steam profile.

The guide currently doesn't include commands from third party plugins, we might add some popular ones later but no promises.

3/23/2020: I haven't worked on this in months so I'm just uploading it in its current state because why not.

mp_friendlyfire - If enabled, allows players to inflict damage on their own team mates
Default: 0 (disabled)

sv_gravity - The gravity of the server, effects all physics objects
Default: 800
Range: Indefinite

mp_flashlight - If enabled, allows players to toggle a flashlight
Default: 0 (disabled)

mp_autokick - If enabled, will kick idle players, team killing players and players that have killed the hostage threshold amount (mp_hostagepenalty)
Default: 0 (disabled)

mp_hostagepenalty - Threshold of which that when a player kills this many hostages, they are kicked from the server if mp_autokick is set to 1 (enabled)
Default: 5

mp_roundtime - How long each round in minutes takes
Default value: 5
Range: 1 - 9

mp_freezetime - How long players are frozen in their spawn at the start of each new round
Default value: 6
Range: 0 - 30

mp_round_restart_delay - How many seconds it takes after a round is finished until the next round begins
Default value: 5
Range: 0 - 10

mp_c4timer - How many seconds the bomb takes to detonate once it has been planted
Default value: 45
Range: 10 - 90

mp_chattime - How many seconds after a match is over the stats screen will be displayed and players will be able to talk until the server switches to the next map.
Default value: 10
Range: 1 - 120

mp_buytime - How long players can purchase weapons until the shop is closed during a round
Default value: 1
Range: Indefinite

bot_add <t|ct> <type> <difficulty> <name> - Adds a bot to the game and matches them to the following criteria if specified.

bot_add_ct <type> <difficulty> <name> - Adds a Counter-Terrorist bot to the game and matches them to the following criteria if specified.

bot_add_t <type> <difficulty> <name> - Adds a Terrorist bot to the game and matches them to the following criteria if specified.

bot_quota - Total amount of bots in the server, to regulate how the bot quota is used, see "bot_quota_mode" below.
Range: 0 - 40 (anything above 32 will usually glitch on official maps)

bot_quota_mode - How the bot numbers are managed in the server. The allowed values are "normal", "fill", and "match".
If set to normal, the amount of bots specified in the quota will be present.
If set to fill, the bots will be replaced by players.
If set to match, the server will keep a 1:N ratio will player and bots, where N is the bots.
Default value: normal

bot_difficulty - Sets the difficulty of bots joining the game, 0 is easy, 1 is normal, 2 is hard, 3 is expert.
Default value: 0
Range: 0 - 3

bot_defer_to_human - If set to 1, bots will not complete objectives(defusing, hostages, planting, etc) unless no human players remain on their team.
Default Value: 1

bot_chatter - Determines how the bots will communicate with each other. There are 4 values which include: off, radio, minimal and normal
If set to off, bots will be completely silent.
If set to radio, bots will use the pre-determined chat menu(hotkeys are Z, X C) to communicate.
If set to minimal, bots will mimic players with mic chat but only relay crucial information.(ex: where bomb was planted)
If set to normal, bots will mimic players with mic chat and will regularly talk and mimic conversations.(ex: notify team of specific weaponry enemy is using, where large amounts of enemies are, death sounds, cheering after clutching, etc)

bot_kick - <all> <t|ct> <type> <difficulty> <name> - Kicks a bot if specified, or all bots from the server.

bot_kill - <all> <t|ct> <type> <difficulty> <name> - Kills a bot if specified, or all bots in the server.

bot_randombuy - Higher difficulty bots have specified weapon choices, if this is enabled, bots will purchase random weapons instead of the specified loadout choice.
Default value: 0 (disabled)

bot_eco_limit - Bots will not buy anything if their money falls below specified amount, if set to 0, bots will not eco.
Default value: 2000

bot_prefix - Prefix the bots will have in the server, there can be four different prefixes.
Your own custom name.
<difficulty> Will list the bots difficulty as its prefix.
<weaponclass> Will list the bots weaponclass as its prefix.
<skill> Will lists the bots skill number(on a scale from 0-100) as its prefix.

bot_auto_follow - If set to 1, bots with a high co-op level may automatically follow a human player if they are nearby.
Default Value: 0

bot_dont_shoot - If set to 1, bots will not fire weapons.
Default Value: 0

bot_flipout - If set to 1, bots will just run around randomly.
Default value: 0

bot_walk - If set to 1, bots will only walk and not run.
Default Value: 0