I had done LDR (different countries) with only one weekend together ... it was difficult, and it never felt like I really got to know him (he was also extremely private, so getting anything out of him was like pulling teeth). The loneliness was always there, but spiked during different times of the month (lovely things, hormones). We had to end it because of the distance, finances, and his health.
I do not miss him as much during the day because I am busy with my job and other things. Nights are when we would spend time together. So the having time to think and not having the routine of spending time together causes me to be more lonely at night.
I'm the oddball, here. I like sleeping alone pretty often, even when living with a partner, or just having quiet alone time at night.
The late afternoons and early evenings are the worst for me. I miss bouncing dinner ideas off someone, going on a walk together, talking about my day, being social, cuddling, and "honey-I'm-home sex" as soon as they walk in the door.
Definitely night. Miss having him in bed of course. But also miss him at odd times during the day when something happens or I see something he would like. Technology helps for sure. Cell phones, texts and Skype make a huge difference.