I have 1 road bike with 650c (Trek 2000 older bike) and a Felt F-5 with 700c. As far as the wheels don't know if it really makes that much difference. The F-5 fits me better (bought the Trek used and the Felt new). The biggest difference really is that the 700c are much more common so if you are riding with a group and get a flat you are much more likely for someone to have a tire if you didn't bring one. With the 650c you'd most likely better make sure you have a spare with you.

Now for the triple vs the compact double. Again the Trek has the triple and the Felt has the compact double. Personally I like the triple much better. I just am not nearly as happy with the gearing on the compact double and may change it to a triple at some point in the future.