Is there a big difference between a PCIe SSD and a regular internal SSD?

You are better off getting a 250 GB SSD for our OS and programs. The 120 GB SSDs typically use half the number of flash dies of the 250 GB, so perform slower. The 250 GB SSDs were maxing out SATA 3, so the 500 and 1 TB SSDs are not appreciably faster typically.

As for SATA vs PCIe, unless you are regularly reading/writing large files (e.g. video editing), it's not going to make a noticeable difference. There are three huge factors working against PCIe SSDs.

1) The vast majority of the speedup when you switch to a SSD is from the small file read/write speeds. HDDs can hit about 150 MB/s sequential speeds. SATA 3 SSDs can hit about 550 MB/s. So they're less than 4x faster. So why do SSDs feel so damn fast?

Because HDDs can only hit about 1 MB/s at 4k read/write speeds. SSDs typically hit 30-70 MB/s, and can top 300 MB/s if you can take advantage of NCQ (process multiple read/writes simultaneously). 50-300x faster than a HDD. *That's* why a SSD feels so much faster than a HDD.

But right now SSD 4k speeds max out at around 300-400 MB/s. It hasn't even reached the SATA 3 cap yet. A PCIe drive has zero advantage when reading/writing small files. In fact with most drives, SATA 2 is fast enough to derive most of the benefit of switching to a SSD.

2) We don't perceive SSD speed in MB/s. We perceive it as wait time - sec/MB. If you have to wait a long time, the drive feels slow. If you have to wait a little time, the drive feels fast. Because wait time is the inverse of MB/s, that means the bigger the MB/s number is, the less difference it makes. Consider reading a 1 GB file.

125 MB/s HDD = 8 sec
250 MB/s SATA 2 SSD = 4 sec (4 sec faster)
500 MB/s SATA 3 SSD = 2 sec (2 sec faster)
1000 MB/s PCIe SSD = 1 sec (1 sec faster)

See how each you double MB/s, the reduction in wait time is only half the previous doubling? Basically, a SATA 3 SSD has already given you at least 75% of the wait time reduction compared to a HDD you can ever get. Even if we were to invent storage medium which could respond instantly, the wait time reduction (2 sec) would be less than the wait time reduction we got switching from a HDD to a SATA 3 SSD.

So why are benchmarks done in MB/s? Because if you benchmark in seconds, the results are really, really boring. Pretty much all the SSDs end up almost the same, with very little difference between the fastest and slowest drives. Review sites have to use MB/s to show any difference, otherwise people will stop reading the reviews and they will lose ad revenue. Manufacturers have to use MB/s to exaggerate the speedup of their latest technology.

http://techreport.com/review/28050/intel-750-series-solid-state-drive-reviewed/5

3) The *slowest* thing your SSD does has the biggest impact on how long you have to wait. Consider a SSD which has 500 MB/s sequential speeds and 50 MB/s 4k speeds. Give it a task where it has to read 1 GB of sequential data (copying a movie) and 1 GB of 4k data (starting a game).

1 GB / 500 MB/s = 2 sec (sequential)
1 GB / 50 MB/s = 20 sec (4k)
Total time = 22 sec

Now say you get a PCIe drive which doubles the sequential speeds to 1 GB/s.

1 GB / 1 GB/s = 1 sec (sequential)
1 GB / 50 MB/s = 20 sec (4k)
Total time = 21 sec

Wow, a whopping 1 second reduction (4.5%) in the overall operation time. Whoop dee doo.

Now instead say you get a SSD which has just slightly faster 4k speeds of 70 MB/s.

1 GB / 500 MB/s = 2 sec (sequential)
1 GB / 70 MB/s = 14.3 sec (4k)
Total time = 16.3 sec

A 5.7 second reduction (26%) in the overall operation time! If you want to decrease wait time, you want to get a drive whose *slowest* speeds are faster relative to the competition. PCIe doesn't help anywhere near as much as getting a SSD with faster 4k speeds.

This isn't to say PCIe is useless. There are a few specialized tasks (like video editing as I mentioned before) which will benefit from the higher sequential speeds. But for most tasks, you want faster 4k and 512k speeds.