This is a common issue on the Raspberry Pi, especially seeing as the hardware on a model B is only a 700 MHz ARM11 ARM1176JZF-S core (simply put, 700MHz CPU) and a Broadcom VideoCore IV GPU with only 512MB of RAM. Tack on an SD card that only has a minimum speed rating (read/write if I'm not mistaken) of 4 MB/s, and you have a system that isn't exactly built for speed.
To put this into context, the iPhone 5S has a 1.3 GHz processor (CPU 1.84 times faster than a default, non-overclocked Raspberry Pi) as well as a quad-core GPU and 1GB of RAM (double the Pi's 512MBs.) So, if you really need a lot of speed, the Raspberry Pi isn't a first choice.
Here's another question regarding speed that you may find interesting. I also answered that one, but there are plenty of other answers that include interesting points.
SD Card Speed
As for the applications taking a while to load (and I'm guessing files as well,) that can be caused by the SD card class.
Class corresponds directly with the minimum performance of the card, up to Class 10. Thus, your class four has a minimum speed rating of 4 MB/s and so is obviously slower than a Class 10 with a minimum speed rating of 10MB/s. However, class isn't necessarily the root cause of your issues. Class is a poor rating and mainly applies to cameras (photo and video.) The higher classes move larger files (HD pics and video) faster, but small files like scripts, software, config files are often accessed faster on a Class 4 than a Class 10.
The first way you can really speed up your Pi is to overclock. You can do this on the first boot or later on with the
raspi-config command. Overclocking isn't that complicated, you can choose one of five options (None, Modest, Medium, High, & Turbo.) Save these settings and reboot.
This is the easy, mostly safe method. There is also another, more manual, more control method which is a bit more complicated and involves manually editing config files and testing to make sure it won't crash. You can read a much more in depth explanation of overclocking and how to do it on the eLinux RPi page.
Overclocking not only makes the CPU/GPU faster, it also increases the RAM speed, thus overall increasing system speed. However, it will run much hotter and will possibly break sooner than a non-overclocked system, because it is running hotter and faster.
If you overclock other than by raspi-config, you run the risk of tripping a hardware, on-way switch that detects over-overclocking beyond the values in raspi-config.
If you want to find out info about your Pi's current setup, you can run
vcgencmd get_config arm_freq and it will give you the current speed of your CPU. If you want even more info, run
vcgencmd get_config int and it will spit back the CPU speed, RAM speed, the core speed, the current setting of
disable_overscan (possibly the root cause of your overscan issue is that this setting is being changed right?), the boot delay, and temperature limit.
Basically, if you want a faster system, you are going to have to possibly get a better card (not necessarily class 10 though) and overclock (which will reduce the Pi's lifecycle). You can add heat sinks which will lift the heat away from the SOC (System On Chip - Contains CPU, GPU, RAM...) and other things that get hot. A fan really isn't necessary, heat sinks will do the job just fine. For that matter, anything that conducts heat and lifts it farther away from the source (SOC, Ethernet, etc.) will work. For example, I use two pennies stack on top of each-other which then touch two more stacked pennies and it works great! What it looks like
Pennies == P P P
RPi Board --> _____________-----_________-----______