I don't think the commas are the problem; instead, the problem is probably knowing the best places to put sentence boundaries.
As RegDwight says, there is no actual grammatical rule that says a sentence must only be a certain maximum/minimum length or contain a maximum number of clauses, or else it is wrong. So, there can be certain circumstances where a very long sentence is the best kind of sentence for something. However, I find that this is a reasonable rule of thumb for constructing a sentence (a "rule of thumb" is something that is helpful, but shouldn't be considered unbreakable):
- Don't have more than two independent clauses in a single sentence. (And remember that having and, but, etc. doesn't always mean you have two independent clauses.)
Look at these three examples (independent clauses are in brackets):
[Having a good memory, I remembered the way to get home], but [I have had a poor sense of direction for as long as I can remember].
[I am tired and hungry in the afternoon], and [because of this, I make a lot more mistakes at my job].
[I try not to create run-on sentences], [but it is difficult to avoid doing so], [and my friends always make fun of me for it].
In (1-2), we only have two independent clauses, and I think most people would agree that these sentences do not run on too long. In (3), there are three independent clauses, which breaks the rule of thumb; some people might say that this sentence is not too long, and some might say it is. I break this rule of thumb all the time — the point is that if you follow this rule, you have a reasonable amount of expressive freedom without having to worry if your sentence might be too long.
If you want to show a connection between two complete sentences, but using a comma violates the rule of thumb, you can use the semi-colon. For example, you could repair (3) by doing the following:
I try not to create run-on sentences, but it is difficult to avoid doing so; my friends always make fun of me for it.