So, I picked up this table pretty cheap from some guy on craigslist. It's in pretty good shape, few dings, some marks, etc. Looks to be pine, no veneer, just stained/finished.

I wanted to make it look a bit nicer and use it as my kitchen table, so I sanded down the top with an orbital sander. Had to work a few spots a bit more than the rest of the table because of dings/marks/etc.

Once I put a coat of stain on it, those spots turned out darker than the rest, obviously I didn't remove enough of the previous finish/seal on the rest of the table.

So, my question is, what do I do now to make this table look ok? Do I need to use a stripper and take all the finish off the whole tabletop and stain again, or should I just sand it down again and throw another coat of stain on it or do I need to get a darker stain and use that?
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When I refinish furniture, I like to leave some of the "natural imperfections" alone. To me it gives the piece some unique character. I do, however strip the entire piece down to bare wood before refinishing. If a "natural imperfection" remains, so be it.
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You did just exactly what you thought you did. All you can really do is get a heavy grit and take the top down to equal depth. Then go with a finer grit and a finer grit till you're happy with the surface.
I have a belt sander that makes a job like that last about ten minutes. It takes longer to change belts than it does to sand a surface. With a palm or orbital sander it'll take forever, but it is what it is.
Regardless, once you stain, the wood is liable to take up stain differently, especially if it's pine. Knots and pitch pockets laugh at stain, but that does look more "natural" than a spot you dug out with a sander.
The reason I mention it is that you may go through all the extra work only to end up with the same results. If you can live with it, leave well enough alone.

You can also try to stain the rest of the table less the spots and see if they'll take a heavier color, but I wouldn't expect too much.
Good Luck!!! :-)
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I have had luck in the past bleaching the dark spots with a 75% bleach solution.
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Scott is right, wood is naturally porous, and natural imperfections and density will cause stain to absorb at different levels, resulting in "blemishes." It's unlikely that a wood like pine will ever stain evenly unless you're going for a near-black finish.

I have had luck in the past with dark areas just re-staining the lighter surrounding areas to bring the color up some, but often that's not possible if the problem arises from knots.

There are products that are designed as an "in-between" layer for projects with soft woods. They paint on and provide a more dense and balanced surface for the stain to absorb into, but they also kill the natural look of the wood. I don't recommend them, as they're expensive and a pain to work with.

Personally, I'd wipe a few coats of stain on it, set it out in the sun for a day, then give it about 8 coats of clear poly, sanding between coats with a fine grit paper, and the end result will be a nice, "rustic" look.
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I'd take a belt sander to it and then Minwax the top, but that's me. I think poly would look silly even if I went with satin. It's kinda like polishing a turd. I do understand what you're after, trying to stop water marks and rings. I think I'd just accept that and use placemats. Some rings add character. :-)
To keep "the look" through the whole table, you'd have to refinish and poly the whole thing. If it actually is pine, and it's probably soft maple or something of the like (who makes tables out of pine?), it's just a tough project, period.
Even tougher to assess the finish without seeing the piece, ya know?
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