Here's the rundown.

I have a Line 6 Spider III half-stack (Yep. I know... Hush )

Anyway, I'm buying it off my brother because he's gonna sell it anyway and it's the only amp I have at the moment so... Line 6 or nothing at all? I'll take Line 6. Anyway, I won't be able to get a better amp for a while so I've been saving and scrounging a little cash here and there and I wanted to get a Metal Muff or something to at least improve the sound a little. But I got thinking: What about an MXR 6 band or something? Would it be worth it to try to modulate the amp's sound/tone itself or just mask it with a dist. pedal altogether... I really don't know. I'm a little embarrassed to ask this, but hey, the only bad question is the one not asked!
From my experience with Line 6 amps I'd go with the EQ. I have an old Spider combo and previously had an HD147. Both take an EQ just fine. As for a distortion, you can run it through a clean channel but it really doesn't sound..."right". So in short, go with an EQ, the amp will still be the amp and you can tweak the sound more to your likings.
EQ pedals are quite awesome, they make a big difference with the sound. The distortion pedal won't really make it sound much better, only a ton of unwanted feedback.

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metal muff may come in handy in the future when you get a different amp, but the EQ would do wonders to a Line6 if you are a tone-nazi. I like the MXR. Quiet and effective. Something you will probably use forever no matter which amp you have