What Firah, said. Yeah.
Tom's introduction into the show was logical, I think, because teenage high-school students normally find girl/boyfriends at some point. It was also an unmitigated disaster for the private world Daria and Jane shared, because same-sex friends nearly always find that when romance appears, the friendship withers. Brittany put it best in her advice column in "The Daria Diaries" when she responded to a suspiciously familiar situation:
"Dear Brittany, I like the same guy as my best friend. What should I do? Feeling Guilty. "Dear Guilty, I'd go for the guy. Once you have a boyfriend, you don't have much time to hang out with other girls, anyway."
Most of us look pouty when we can't be with a friend who's dating, but we always have other friends, and we go out with them instead. Besides, when it's our turn to get a Significant Other, we can dump everyone, and they'll understand and cope because they have other friends, too.
Daria and Jane, however, do NOT have other friends who share anything at all like what they share with each other. No one else understands their alienation, anger, frustration, and cynicism. No one else accepts them as they are, as they do each other. They have no other close friends at all. The entire show was constructed on this foundation. "There's this one girl named Jane who is snide, antisocial, and resentful," Daria writes in her diary after moving to Lawndale. "Finally, a friend." Trent did not pose any real threat to the relationship, Trent being asleep so often and so clueless about Daria's crush on him--not to mention being Jane's sister, making them the perfect package deal for Daria if Trent had only noticed her (ignoring problems like statutory rape laws).
Tom was different, a ten-megaton blast of lethal radiation washing over a double-island paradise. Jane is gone with Tom, Daria has nothing to do. Then Daria is gone with Tom, and Jane has nothing to do. Both feel the old loneliness creep back. Tom's cool and cynical and a good kisser, but he's just not like [fill in the blank]. You don't know what you've got till it's gone, and there is a grave danger that it is really, really gone.
Yet even through their nuclear winter, Daria and Jane still try to make their friendship work. They don't give up. How many people--seriously now--do that? And they pull it off (thanks to the script writers). "Boxing Daria" highlights how far Tom has begun to drift from Daria's heart and mind, and how critical Jane has once again become to Daria's mental health and emotional well being.
College life is certainly different, and Daria and Jane would know that they were going to be apart more often (though still in the same city). There would be more opportunities to meet guys. And they might have no problem with that--jeez, everyone likes to kiss and be kissed. It's like having your passport to humanity stamped. Ya gotta do it. However, one would think that in the post-Tom world, Daria and Jane would have worked out an ironclad new priority: Their friendship comes first; guys (perhaps even husbands) come further down the list. And if someone doesn't understand that, the door's thataway, don't let it hit you in the ass when it shuts. Daria and Jane might be more strongly inclined to move together when big moves must be made. If they've fought so long to stay in each other's life, why stop now? (We're their scriptwriters now, you see.) That which does not kill us won't necessarily make us stronger, but we will damn sure be prepared for it the second time it shows up.
I think it is tempting to turn Daria and Jane into lesbians in fanfic as a way of armoring them against future Toms, or because, well, why the hell else did they want to keep each other around when they could have had a GUY, forgoshsakes? Like any of us straight people would have even bothered to try keeping a best friend around. You could probably do a good Daria/Jane slash story and make it click, though you would have to add a mountain of backstory all the way back to the kind of books Daria checked out as a child with her adult library card, adding entirely new lines of mental dialogue to every scene, whole new scenes that never happened, etc. Why bother?
Seeing Daria and Jane as halves of a whole makes so much more sense, and it's so easy to run with. And it makes them so much more rare and wonderful as characters.