The proportional space between notes and rhythms is one of the arts of typesetting (or handwriting) music. If the spacing is off, bars are crowded, notes of equal rhythmic value are uneven, and in the worst-offending cases, poor spacing can make the music unnecessarily difficult to read. When I prepare session music, the goal is to make it impossible to be misunderstood—and one of the easiest ways to convey rhythm quickly and accurately is to set it properly.
In olden days, music spacing needed to be determined by hand, and in advance of setting system. How could you know to space the first two notes if you haven't considered the contents of the entire system? Thankfully, computerized notation has transformed this process in the same way the word processor took the painstaking effort of formatting text across a whole page. For the most part, Finale and Sibelius do a good job of spacing, but you have to let it help you. It's way too easy to force too much into a system, resulting in the above-described spacing problems.
In my work, I like to look at each system and begin with the smallest rhythmic value and give them all equal spacing. Once that's set, look for the next smallest and do the same. Continue up the rhythm values as far as practical for your setting. I've mentioned before that I engrave by feel, and since notesetting is a long series of compromises, you'll inevitably encounter a situation where you need to use more of your aesthetic intuition than rules from a book.
Getting notes spaced properly is easy. Recognizing the problem and reducing the amount of music on that line is the part that takes a bit of thought. What if you're up against a tight page turn and you just cannot push that page-turnable multi-bar rest to the next page, but you just have too much on a particular system? Reducing the number of bars per system is out. What to do next depends on the severity and frequency of the issue across the piece. If you're stuck in just a few spots, consider using a tighter rhythm spacing for those effected sections, keeping in mind the entire line, and the context; try not to have overly tight passages adjacent to loose spacing.
If everything in the score is too tight to make work appropriately, your options are to either adjust your expectations of how much you can fit to a page, reduce the staff size to a size that will allow accurate spacing, or a combination of the two, giving the best result for the size. I should add that rhythmic shorthands such as bar repeats or measured tremolos can be helpful in solving some issues if your project allows them to be used, and/or if the music lends itself to them (i.e., things on the page repeat themselves).
Now that you have your systems well-spaced, did you consider lyrics and chord symbols? Lyrics are a funny thing, the note length is the same, but the spelling of the syllable can be one letter or many. Your spacing needs to absorb lengthier syllables in a way that doesn't throw the rest of the system way off. I have found a good way of forcing myself into good lyric spacing is to disable Finale's function that automatically considers lyric length in its spacing of the line. This way, the music alone is spaced properly and any lyric collisions that occur are my problem to deal with. When this function is enabled, Finale will first make all of your lyrics fit on the system, then space the music, resulting in potentially poorly spaced systems. Chord symbols pose the same problem, especially if you're working with jazz composers like I do; some of those chord extensions are long and will throw off your ideal note spacing.
Correct spacing will immediately give your music a more published look. Always keep in mind your role as the engraver, never let the layout of the music come in the way of a good performance.