When I'm reading and I come across a word I don't know. I have the habit of reading it with the English word "something".

For example, if I didn't know 魚 and I read 猫は魚が食べる, I'd read it in my mind:
"neko wa something ga taberu".

That's not good since "something" is a very un Japanese word, so what is a better way to read such things when you don't know how to read them?

How about "naninani"?

Jones beat me to it

Personally, I would look up the word in a dictionary(for ex. Nintends DS Japanese Dictionary) and enter it into Anki. And then keep on going. As long as I know the words meaning, I'm OK.

Although since I tend to read manga(with furigana on top of all the kanji), I never really run into your problem.

I used to do that as well; one could render unidentifiable words as 未知の単語 (michi no tango; unknown word/s) or unidentifiable kanji as 未知の漢字 (michi no kanji; unknown kanji). When I've been out of practice, I usually substitute what I don't know with "blank" or better yet "...". It might be best of all to leave it soundless, as in the last example, because then you're not associating it with any particular sound until you find out it's actual pronunciation and/or meaning.

[ファブリス]

I like うん ! (the way Japanese acknowledge something sometimes in conversation, doesn't really sound like the written version though).

You can imitate a buzzer sound too, if you're bored (you know like on TV game shows when the participants get the answer wrong).

If you're getting really annoyed at all those readings you can also imagine that *beep* sound they have on TV when someone is cussing. Even better, have a portable one (perhaps you can get one on a keychain or something). Just press it whenever you can't read a japanese character!

How about なんとか?

I say 知らない漢字.