Lets get the worst parts out of the way first:
Distance obviously, being away from the person you love is fucking tough. Some days you just need a hug and you can't get it. You feel empty and you get this horrible ache of just needing your SO but not being able to have him/her. Also the lack of sex/physical side of things can be horribly frustrating. It's easier now with Skype, snapchat, texts etc. but still never the same as the real thing. Not being with them for important things: anniversaries, birthdays, christmas etc. is tough.
Money. Every time you are arranging a visit, it usually ends up costing a small fortune. So you're constantly chasing your tail. I'm trying to save up to move to my SO but at the same time every time I visit him that basically empties my account and I have to start again.
Jealousy/Anxiety/Arguments. Everything like that is amplified when you are in a LDR. Tiny little niggles can end up being huge big arguments if you're not careful. You have to keep the lines of communication open 100%. Try not to go to sleep angry/not talking to each other. When you argue when you're physically with the person it's so much easier to get over it, but when you're not with the person it seems to snowball into something much bigger if you're not careful.
Saying goodbye. Don't need to say anymore for this one. It just sucks. =/
That's the basics of the bad things. Probably lots more that I've not thought of but partly because I'm typing this quickly in work lol.
Good things!
I'm gonna say distance again here. Not being physically with the person means you have to focus on the mental side of your relationship which I find good sometimes. It's easy to get carried away with sex and focus on that a bit too much in a relationship where you are both together but obviously with long distance you can't do that. I feel so in tune with my boyfriend thanks to the long distance, more so than I have done with any other relationship I've had. We know each other so well.
Seeing them! Holy shit that excitement you feel as the days get close to you seeing them again is the most wonderful feeling ever. That first hug and kiss, the first night together sleeping next to each other again. You appreciate all those kinds of things so much more. In fact it makes you appreciate your other half in general so much more. You won't be able to take them for granted because you know how hard it is when they're not there.