My boyfriend is an independent consultant, so he pretty much sets his own policy. For per diems he uses the IRS guidelines. For hotels, the client usually has preferred hotels. If not, we use Quikbook or another similar site to find good deals. In general, he usually picks something around $100 in smaller cities and something under $200 in NYC. Location is a big consideration that comes into play.
Often, he selects a hotel that has a kitchen and serves complimentary continental breakfast (Flathotel in NYC, for example). Most travel expenses, including a set per diem, are usually negotiated into the contract with the client upfront. So he draws out the per diem for the week on Sunday, eats lunch somewhere reasonable, then prepares dinner in the kitchen at the hotel. Whatever is left at the end of the week goes into savings. This works out very well.
If I come up to visit for a weekend, I fly up on points, and the client is usually amenable to covering the weekend hotel stay instead of flying him home. This also allows for a saturday night stay which may help reduce the airfare.
For keeping up with receipts, he brings along a roll of scotch tape and several sheets of blank paper. He takes each day's receipts and tapes them to the paper, then labels and dates each sheet. If needed by the client, he photocopies each sheet to send to them. All sheets with receipts go into client files when he gets back home.
He's been traveling each week for 6.5 years, so he has his systems and routines locked in now.