I replaced the widows in my house this spring, and you're asking a lot of the same questions I asked.
First, the cost of the windows themselves is only part of the equation. You also need to consider the removal of the old windows, installation of the new ones, and the finish work - because chances are, all the trim, and all of the interior sills will also need to be replaced. Installation can actually be 50% of the cost of the job, and a poor installation will ruin any value you might get from buying a top-notch window.
There are a few things to consider when looking at the windows themselves. First, as you point out, is the construction. I ended up going with vinyl - again, a quality vinyl window and a cheap vinyl window are two different things - the local shop here had examples of a number of different windows cut open so you can see the difference. Cheap windows may not be insulated, or may be made up of different pieces glued together, rather than a single extruded piece.
Next, the glass. You can get single, double, or even triple panes. Some use argon between the panes, some don't - the sealed, argon-filled windows offer better insulation. Then there's the low-e coating on the glass - it can be applied in different ways, which will affect the durability and effectiveness of the window.
You need to consider casement vs single hung vs double hung. Are they on a 2nd or 3rd story? You'll probably want to get a window that allows you to clean the outside without having to get up on a ladder - most double-hung windows will allow you to clean it from the inside of the house. If you're putting windows into a bedroom, you have to allow for a certain size for egress - you may need to go with a casement window in that case.
The bottom line is, check around - get at least 3 estimates, unless you're planning on installing them yourself. See what's included in the estimate - one of our estimates included a single line item for "Installation", while another had 3 pages of details, down to the number of board-feet of trim, cans of foam insulation, and the cost of the building permit. Guess which one we went with?
Is it DIYable? Yes. No. Maybe?
You may find that you start the job, everything works out just right, and you complete the work in record time and under budget. More likely, you'll run into a bunch of unforeseen problems, take 5 times as long as you'd expect, and end up way over budget.
The best way to tackle DIY work that you are not sure about, is to have the resources available to quickly fix mistakes. In your situation, it might be a good idea to purchase a replacement window before you begin. If you damage the old window beyond repair, you'll simply have to install the new one. On the other hand, if the repair works out, you can return the new window you purchased.
It also never hurts to have somebody with knowledge in the type of work you're doing, so if you run into trouble they can offer guidance.
If you come across something you are really not comfortable with, there are always professionals available to do the work for you. You might also be surprised that they charge less than you might think (not always the case, but does happen).
Best Answer
The inside of a typical vinyl window frame will have spaced out chambers separated by vinyl webbing as a thermal and drainage system. The sill track channel of the windows should always allow water to drain, if water enters into the track a small hole will direct water through the frame and out the exterior weeps.
If a screw is drilled through the entire frame of a drain chamber water could possibly leak into the framing below and possibly cause dry rot or moldy insulation. I would not recommend drilling anything through the entire frame of a window sill, I've seen it too many times cause damage in just a couple years. Hardware through the first layer of vinyl, probably nothing to worry about. Its common the first layer of vinyl is used to attach hardware even on the sill.