I tend to update my fitness routines over time as my needs change and as I improve my understanding. One important goal with the most current revision of my workout schedule was to minimize the risk of injury. I had knee surgery last year and during the months that followed had to be very careful to not cause additional problems. What follows is based upon several references, which I shall list at the bottom of the article.
In addition to general health benefits like maintaining a healthy body weight and reducing blood pressure, any complete fitness routine must improve strength, endurance, and flexibility. The body quickly adapts to various physical routines so it is important to introduce plenty of variety in your workouts. Also it is especially important as you age to allow sufficient time to recuperate between strength workouts. I think my current schedule is a near-perfect implementation of these goals and considerations.
In a nutshell
I do strength training every four days. On the three intervening days I do various swimming, biking, and running routines. I stretch after every workout unless I'm really pressed for time. I introduce plenty of variety in both the strength training and the cardio workouts. I workout for at least an hour every day unless I'm excessively sore from a previous workout.
For advice and planning of strength training routines, I'm very fond of The New Rules of Lifting, by Lou Shuler and Alwyn Cosgrove. This book is easy to read and gives you the information you need to work out safely and efficiently. There is an edition for women as well.
I like a mix of the traditional triathlon sports: swimming, biking, and running. For each of these three sports I work in a mixture of low and high intensity training. Low intensity is just as it sounds. You just go, slow and steady, until the allocated time is up. High intensity is also not complicated and my favorite high-intensity cardio activity is sprinting. This applies to all three sports.
No matter which sport I'm training in on a particular day (and this applies to strength training as well as cardio), I'm always careful to warm up for about 10 minutes. So here is an example high-intensity swimming workout.
Swim easy laps for 10 minutes to warm up. Then for the next 45 minutes I do the following: swim one lap as fast as I can (sprinting), followed by 4 laps nice and easy (recovery). Then repeat. After 45 minutes of that I finish with 5 minutes of easy laps as a cool-down.
I'm fortunate enough to have a great gym to workout at. In additional to superb facilities, they offer various group training programs. One of my favorites is spinning and I try to work in at least one session of that each week.
I don't have to time to stretch after every routine, but I do stretch if I possibly can. I also take mini stretch breaks at the office during the day. I don't think it matters what specific routine that you do so long as you remember to take your time. Ease into each stretch. Do it after your workout when your muscles are warmed up.
The best workouts in the world can be sabotaged by poor diet. I've read a lot of books on the subject and most current stuff is a variation of the Zone diet by Dr. Barry Sears. So as a rule I try and follow the general principles of this diet and eat smaller, more frequent portions (as opposed to fewer and larger ones) throughout the day that contain a good mix of low-fat protein, good carbs (fruits and veggies), and healthy fats. It's pretty simple.