Up until now I've only used console commands once- to get rid of the glitched Motor-Runner's Helmet that was permanently stuck in my inventory after I completed the quest. But now I'm starting a new game, and I'm thinking of adding a couple of items to speed things up a little in the beginning. Nothing major, just a couple of Varmint rifle mods that Chet could've sold me at level 1 anyway if I had a luckier roll at his inventory. Maybe a Patriot's Cookbook as well. Fallout Wiki warns that console commands can cause glitches, but I am hoping it mostly applies to things like forcing quest completion or resurrecting killed NPCs. Does anyone know for sure which console commands are "safe"?

On the most as long as you shy away from quest specific items ( those marked as quest ones ), then it should be safe.

Over the years I've added a bunch of stuff and never had a problem, except when it was not real items ( Baldurs gate had some great non items ), or quest items.

As madocmayhem said, stay away from quest items. This also includes perks added by quests and challenges.

There has recently been an addition made to the Vault Wiki for the console specific to New Vegas:

"WARNING: Using console commands in the Steam version of Fallout: New Vegas will prevent you from obtaining achievements for that session! To re-enable them, exit the game and start it again. Make sure you do this before completing a quest or achievement. Furthermore, changing any of the values described here, save those which are extremely minor (like adding items, experience, caps, etc) will likely cause bugs in your game. You have been warned."

Since they are in the process of merging the different Console pages under a generic Gamebryo Engine page this may not remain long. But take heed. It is my experience that Obsidian did not implement all of the commands and seems to have implemented some slightly differently.

Generally speaking it is safe to spawn items not required by quests, removing the quest marker from an item once the quest is completed, and fiddling with your PC's stats (as long as you stay away from the 'set' command.)

While adding items via the console is almost always a safe thing to do. I always work off a Forked Save when using the console on a character (not in game for things like TCL, just changes to the character's inventory or skills). While the chances or borking things are small, it is always best to have a pre-console save to go back to just in case.

As stated above, if you care about achievments, after you enter the console commands, and are satisfied, then save in a new slot (forking the save) then exit the game, and restart it. Also, not all bad things that can happen to your character from the console show up until you save and reload. Note, the things that have a tendency to mess things up are the character generation menus that you can pull up with the console and messing with Quest Stages (this from using the wrong stage id more than anything else)