GREAT post and some very good tips and advice!!
As someone who has travelled on a shoe-string budget in my youth, I have experienced much of what you mentioned, but as you clearly pointed out, cutting costs CAN actually cost you in the end (time spent travelling/possible missed connections etc), and though in some cases the cheap flight websites may seem like a good option, they are not LIVE realtime, so often additional costs are added, and often the traveller doesn't notice that there is a SUPER long layover or two, which is what makes it cheaper.
though us travel agents can't always beat the website prices, most of us have deals with the airlines (if not, a small service fee is charged by the agent - to cover cost) and hardly ANY of us mark up or charge extra for car rental, accommodation, packages, cruises or attraction tickets as we GET comm, and usually have negotiated rates CHEAPER than the rack rates online....... the added bonus is our knowledge of visas/minimum connection times and destination information.
JUST this last quarter I had 4 different "new clients" request various quotes on various dates, routings and numerous variations of the same package.... 2 weeks later they booked all on the net (saved the equivalent of $60 USD per person on the flights....... not only were connections missed, visas were not applied for in some cases (in which case you are refused entry) - 100% cancellation period for hotels and land arrangements so no refund and had to PURCHASE new tickets home as their cheapie tickets were non-refundable too, and the website connections given were UNDER minimum connection time for he relevant airport
ALL worst case scenarios, yes, but the equivalent of approximately $60 is well worth the time, care and effort your agent will spend making sure your itinerary runs smoothly and all components booked through reputable operators :)
