I grew up in a house with good wood-framed, single-pane windows - plus the add-on storm windows. Our storm windows were easy - you just slide them up after you slide up the regular window. We also had matching screens, and in spring we swapped out a few of the glass storm window panels (frame stays in place) for the screens. Of course, I lived in a colder climate then....
Caulking gaps and adding insulation is going to almost always be a much better use of your time and money than replacing windows, given that you are starting from standard low-end residential construction.
Next, have a look at your ducting! You should have no gaps, missing insulation, crimped ducts, hard turns, et cetera. Usually installers do a real crap job on ducting - the HVAC guys put the new kid on ducting. With flex duct, this usually means sharp turns, loose connections, crimping of the duct with overtight straps, et cetera. Think of a garden hose - if you turn too tight ("kink" the hose) it cuts off the water flow. Same thing with air, but even easier to do wrong since you have a lot less pressure (maybe 1 psi instead of 100 psi.) You want smooth, even, open ducts with gradual curves. Be sure to use the RIGHT tape. There is a lot of crap tape out there, and common "duct tape" or "duck tape" is NOT appropriate. The glue will harden and let go over time. The tape should be foil (metal) - and not the cheapest one at the home improvement store. Find the HVAC expert there by going in sometime M-F, 9-5 when the contractors shop.
If you want to go beyond that, get yourself a can of expanding foam (the latex stuff is safer than the polyurethane - poly pushes HARD when it expands, you have to be careful) try taking the trim off around one of the windows. Installers usually are 'full of fail' when it comes to insulating between the rough-in and window. Use that expanding foam to fill the gaps, let dry, cut off excess foam, reinstall and recaulk trim.
Once you finish with the windows, start sealing all the attic perforations: Again, installers are usually 'full of fail' when it comes to sealing all the holes they cut between the attic and house body. Lights, power, plumbing, et cetera. Someone cuts a rough hole and relies on a cover plate or fixture to block it. Plus, you get plenty of attic dust.
Now that I think about it - here in Texas, attic sealing should probably come before under-trim resealing. Attics commonly get up to 160F in the summer, while it's only 100F outside.