Bethesda themselves release modding tools, and the console is enabled by default, so that suggests that you should be good to go right? Kind of.
Apparently once you issue a console command, you're no longer eligible for achievements until your next session. So if you're worried about achievements, enter your console command 'cheats' (like "fov 90"), save, exit, start up skyrim, load, and be on your merry way.

Sources:
gamasutra review under Console = Cheater
gamefaqs

EDIT: It seems like you may not have to quit in order to get the achievements. Through my own testing, I have used console commands and still obtained steam achievements without reverting to an earlier save. My process:

1. tcl
2. walk through some walls
3. tcl
4. Make an enchanted item
5. player.additem 000bb956
6. player.additem 00023d6f
7. Make a potion
8. Make a piece of armor
9. Save game
10. Exit Skyrim
11. See new "Artificer" achievement

Notes:

• I have the steam overlay disabled.
• I'm using version 1.1.21.0

Previous answer:

Bethesda themselves release modding tools, and the console is enabled by default, so that suggests that you should be good to go right? Kind of.
Apparently once you issue a console command, you're no longer eligible for achievements until your next session. So if you're worried about achievements, enter your console command 'cheats' (like "fov 90"), save, exit, start up skyrim, load, and be on your merry way.

Sources:
gamasutra review under Console = Cheater
gamefaqs