I assume everyone is running into these issues, I want to see how everyone else is handling them.

1) Recently, I've had a few different clients forget to schedule lunch in a busy shooting day. Both times I got the "we're too busy for lunch around here" attitude. Listen, some days when I'm at the office I have to skip lunch, but when I'm on a shoot, lugging sand bags up and down stairs, trying to keep on schedule, and I'm setting up the tripod for the thousandth time - this is not a day to skip lunch. The first time I just blew it off as an a-hole client (although made a mental note not to have it happen again), but the second time (different client) I feel like I need to make plans to avoid it. That said, I don't like to be asking "what's the plan for lunch?" three weeks ahead of time, makes it seem like my priorities are out of whack.

2) I've also had more people wanting me on planning phone calls that they want to schedule a week or two ahead of time. I might have a day free on my calendar, and client wants to do it from 1p-2p on a weekday. I charge them some paltry sum (1 hour on an hourly rate), but then a week goes by and a different client wants to shoot that day (for what amounts to 10x-20x what I would be making from being on a phone call). I feel like a tool for turning down a good paying shoot, but if I cancelled a phone call I'd booked a week in advance because something better came along, it doesn't exactly seem fair to that client either.

So... what is everyone else doing for these two things? If it's not clear, we're a two-man shop, so it's not like Hollywood or anything.

Lunch is mandatory. Period.
Yes, it gets delayed or could be shortened to a 15 minute break but ya gotta eat.
If I'm on a full day shoot, I absolutely discuss lunch plans before the shoot. That way it's on the table (pun intended!)

As for phone calls, if you booking them a week or two in advance, it shouldn't be a problem to reschedule. Paid gigs always take priority for me with the caveat that the call must be successfully rescheduled. If it truly can't be, then the gig needs to be rescheduled.
Same rules apply to prioritizing two clients who want the same time. First to call takes priority but I will always try to keep both happy by shifting schedules if possible. I hate saying no. Sometimes it's unavoidable though! I then offer up one of my friends as an alternative and take a cut for booking it.

Mike,
About lunch. Put it on a shooting schedule on paper or file for the client. Make sure that a lunch break is part of the conversation beforehand and explain why it is a necessity. On conference calls, they would be lower on the priority list than an actual shoot. Reschedule.
JH

Sometimes I have to "sell" lunch to the client, in truthful and practical terms: "We can work straight through if you think it's really necessary, but in my experience the crew's (or my own) performance and productivity significantly drops without a short 15-30 minute break for food and caffeine."

In a couple past cases of gigs scheduled on the same day as a previously scheduled conference call, I've explained before the shoot that I would have a 30-45 minute conference call at such-and-such a time, and that ideally we'd schedule lunch break around that set time, and then explained prior to the conference call that I would have to adhere to the prior set end point and couldn't run over. In both cases nobody involved has minded, but obviously this will vary by parties involved.