B767Driver offered his perspective from a major airline heavy-driver, so let me offer one from the regional side as well. It is a bit different, not only because we fly smaller tubes but also because we jump puddles, not ponds.
Similar to B767Driver, I consider the time between TOC and TOD as "cruise" time. Since we do not have VNAV or autothrottles, we need to be very vigilant about our climb profiles, speeds, and descents. It is easy to get slow in vertical speed mode in the climb, or overspeed the airplane and cause an uncomfortable ride in descent (the airplane pitches very authoritatively to keep from overspeeding). I think it is very important to stay attentive to the airplane during these phases of flight.
Now, in cruise, things do change a bit. We fly mostly in RVSM airspace, and if we are not then it means a short leg where you are pretty busy anyway. By being in RVSM airspace (above FL290), it is recommended we use the autopilot, so we do. This changes the flight from a "flying" phase to a more "monitoring" phase. However, even though we are monitoring the autopilot and not actually "flying," there are still many things we need to do and stay attentive of.
At TOC, I also normally check the fuel on-board against the figures in the flight plan. I do this to see if we may have gotten behind or ahead of our fuel numbers due to a higher-than-normal climb, or a step climb that burned more fuel. This is critical for two reasons: One, if we burned less gas, it might mean we are too heavy for landing. Two, if we burned more gas, it might mean we are getting close to our reserve fuel for the destination or alternate airports. They plan us that tight. Often. Checking this early helps us formulate a plan to either climb or descent to possibly burn or save gas. I'm a "requester," so I'll often look for shortcuts that save us time and gas, so figuring out early that we might need a shortcut means I'll become a pain in the ass to ATC much earlier in the flight.
After checking the TOC fuel numbers, and setting cruise thrust fuel flow settings, that is my signal to consider letting the people up. If it is expected to be fairly smooth, we'll let them up. I hate commuting when the seatbelt sign is on the whole flight. It makes me feel like the crew forgot about us. If it is going to be bumpy, we'll still make a PA telling the passengers this. Two reasons: Then they know we didn't forget about them, and if they get up (they will, trust me) at least they are fairly aware it will be a rough ride.
As a Captain now, it is my responsibility to fill out the aircraft logbook each leg, putting our name, employee number, and departure/destination airports on the page. I find after getting things set up for cruise, this is a good time to fill out everything but the destination, in case we divert. This means it is done early, so that on the ground when things are busy, it is one less thing I need to do. When you are running the parking checklist, getting things set up for the next crew, packing your flight kit, putting away charts, etc., one less task is a good thing.
So after "cruising up", letting the passengers free, filling out the logbook, I'll now normally pick up the arrival ATIS (if they have D-ATIS) or a METAR through ACARS. This will help tell us what runways they are using, what weather to expect, and if it may be bumpy on descent and arrival to let the flight attendant know to clean up early. We also send off and "in-range" message, to get gate information for our flight, and information for where the airplane goes next and where we go next. Just another thing to help us plan. After getting the weather, I'll swap my departure airport charts for my arrival airport charts. I have an interesting way of sorting my charts, so I'll pull them out and "sort" them in the way I expect things to flow. Then we'll begin programming the FMS for the expected crossing altitudes, expected approach, NAVAIDs, operations frequencies, etc.. I like to get these things done early, so we are not heads down searching for a ramp or ops frequency on descent or on the ground. I also like to review the 10-9 chart (taxi diagram) to get an idea of how things will look to me when we clear the runway. This helps me avoid going the wrong direction, or having to stop and look at the chart to figure out where the heck I am after we've landed.
Obviously, you can see this takes up a lot of time. If this was an hour-long flight, this just ate up the whole cruise time and maybe some of the early descent. If it is a two-hour or longer flight, then I'll have some time to kick back, maybe drink a cup of coffee, look out the window, or just chat it up with my First Officer. I enjoy talking with my crews, learning where they are from, their background in flying, etc., because I like talking to people. If they aren't talkative, then maybe I'll crack a book. I don't like reading in the cockpit much though. I definitely don't break out iPods, or read the paper. I find a newspaper is too big and cumbersome, and it blocks my view of the instruments. More often than not, I'll actually pull out a manual and review some procedure or system that I'm lacking on. I figure I'm at work, I'll use that time to review, so when I'm at home I can do all the stuff I really want to do! Professional pilots need to continuously study, and at least at work I can somewhat justify to the Chief Pilot that I was reading a manual in flight.
Also, after jumpseating with a great crew out to PHX one morning, I have taken up the habit of having my enroute chart out and manually backing up our route with VORs. We have an NAV pointer overlay on the HSI, and backing up the FMS routing with the VOR airway seems very helpful at ensuring we do not get off course. It also helps me stay aware of our position over the country, so should something occur where we need to land, we'll know where to go. Not to mention it has helped me learn the various VOR identifiers, so when ATC says "cleared direct Omaha" we go to OVR, not OMA in Bosnia.
So that pretty much takes you through the "boring" time of cruise as a regional pilot. Shorter legs, smaller tubes, but the same stuff really.