Question: How do I keep players from accessing certain commands?
I'm making a server and these kind of things are thing i need to know

Answer: 
By default, the majority of commands (with the exception of `/me`, `/tell`, `/help`, and `/trigger` for some reason) are restricted to server ops. Players are, by default, not allowed to use any other commands on a server. Server ops can use other commands. You can specify ops in the `ops.txt` file, or by using the command `/op <playername>` in the console, or in-game (assuming you have added yourself as an op).

By default, server ops have access to all commands, including commands like `/stop`. You can change this by modifying the `op-permission-level` in your `server.properties` file. Setting it to 4 (which is the default) allows ops to use all commands. Setting it to 3 restricts the `/stop` command, setting it to 2 restricts server moderation commands (`/kick`, `/ban`, `/op`, `/deop`), and setting it to 1 removes all special permissions from ops other than the ability to bypass spawn protection. You can still use all of these commands in the server console.
Adding on to @Unionhawk's answer you could aternatively just use a permissions plugin such as [Group Manager](http://wiki.ess3.net/wiki/Downloads) or [PermissionsEX](http://dev.bukkit.org/bukkit-plugins/permissionsex/) with Bukkit along with the [Essentials plugins](http://dev.bukkit.org/bukkit-plugins/essentials/). I'd definitely recommend reading some guides on running a Minecraft server, [this not the best guide](http://www.wikihow.com/Run-a-Successful-Minecraft-Server) but a guide nonetheless and should point you in the right direction. Just google around to try find a guide that will suit you best in your objective.