Not to complicate the issue but you should really include the Orthodox Church as well.
Some issues that made a difference to me (which is by no means all of it.
Catholics and Orthodox include the original books of cannon. The Protestants have dropped them out. These include what is known to Roman Catholics as the Apocrypha and to Eastern Orthodox as Deuterocanonical books. (these are almost the same with a few exceptions. it is important to note that what was considered cannon was pretty fluid for several hundred years after the time of Christ.)
EO and RC believe the Bible is not the sole athourity on life or God. Church Tradition plays an important role. The Bible was never meant to be a stand alone everything in the world you need to know. Also scripture is to be interpreted through church tradition. Not whatever way our minds percieve it. Most protestants are Sola Scriptura or believe that everything you need to know is in scripture (only the ones they use) and everyone can interpret it themselves any way they want and that interpretation can be their athourity.
The function of a Priest in the RC and EO church is different from that of a protestant pastor. And the services have different functions. The Sunday service for protestants happens for reasons I am not quite sure of. Thats one of the reasons I left

But the Pastors main function across the lines is to preach a good sermon. motivate/teach/inspire whatever but to preach it. The Priests function is to pray and serve the Liturgy/Mass. He does not interact directly with the congregation the same way the protestant pastor does and the sermon is much shorter (as a general rule 15 minutes is considered long winded. usually closer to 5 to 10 minutes.) Also the resons for differents services are clearly defined. In the Orthodox church the Liturgy is for prayer and cluminates in recieving the Eucharist. Same with Mass.
EO and RC are liturgucal. We follow a script for each service. This varies for protestant churches.
EO and RC both believe in the bread and wine turn into the body and blod of Christ. Protestants vary on this.
EO priests can marry if they marry before they are ordained. Unmarried clergy must remain unmarried. Monastics and Bishops etc may not be married. There are also other restriction on marraige. RC clergy may not marry. Protestant pastors may.
the pope. The RC church has a lot of beliefs about the pope that other Chistians do not share. Your best source on this would be the Catholic church. EO believe the pope is just another Archbishop. Back when the EO and RC were part of one church Rome was one of the five principle jurisdictions. The Pope was first in honor amoung equals. Rome insisted he was first in athourity. Do you see the distinction there. it is one of the things that eventually lead the the great schism and the split of the East and West. The four jurisdictions in the East became the EO church and the one in the West became the RC church. The protestants think nothing of the pope.
Church structure and leadership. All protestant churchs have different levels of leadership. from nothing to some fairly structured set ups. The EO and RC have a head and athourity structure on down. The EO have a head for each jurisdiction (Russian, Greek, etc) but we have no Head over them. They are just held together by unwavering adhearance to tradition and the Holy Spirit. The Echumenical Patriarch is the first in Honor (having taken the position of Rome when the split happened) but has no real athourity over the other jurisdictions. just the influence afforded by honor.
Confession. Protestants confess to God if they confess. RC confess in the presence of a priest but do so annonomously (sp?) and are often given prayers or penance to do. EO confess in the presence of a priest, usually the same one (a Spiritual Father who is like a faith guide or coach) and face to face. While they may be asked to do something to help them overcome a sin or complete full repentence (like give back something they have stolen, go to athourities, stop recieving communion for a time) there is no "penance" to do that is like what the RC church does.
both the Catholic and Orthodox church are very specific about what may be used for communion. RC use unlevened bread and wine and EO use levened bread and wine. Protestants use a variety of things.
Both EO and RC practice closed communion. In the RC catholic church you may take communion if you are RC (or EO apparently). in the EO church you may only take communion if you are EO and if the priest does not know you or trust you you may still be denied for any number of reasons. The point is to protect you and protect the priest and protect the Eucharist (remember they believe it is the actual body and blood of Christ!!! This is very serious business!). In the EO if you take communion anywhere else you excommunicate yourself. Sometimes you accidently take communion other places and you can get a blessing from your priest to do so in some circumstances but as a general rule....participating in any sacrement outside the EO will excommunicate you. These are very serious matters and should never be taken lightly. In the protestant church closed communion is rare. In the RC first communion is around 2nd grade I think. In the EO church it starts as soon as you are baptized (which can happen as early as 41 days adter birth). In the protestant church it varies by denomination and beliefes about communion, baptism and salvation.
Speaking of baptism. Both Catholic and Orthodox Christans practice infant baptism. Protestants sometimes do infant baptisms (this was the norm until very very recent history) while others will only baptize those who are old enough to make a choice. "old enough" is subjective and vaires from one church to the next and I have seen anything between two year olds and people who were forbidden until they were over 18. Also what one must do/prove in order to be baptized varies in protestant churches.
Confirmation. Rc practices confirmation as do many protestants. It is a time of owning ones faith and usually happens in churches where infant baptism is practiced. The EO does not practice any sort of confirmation. The baptized are recieved fully into the church at baptism once and for all. Abviously there is no need for confirmation when one is baptized as an adult or where salvation is a moment in time decision.
immaculate conception. This has nothing to do with Christ. RC believe Mary was born without the taint of original sin. She was special. different from other humans who were doomed to sin. EO believe Mary was born as everyone else and chose to live a rightous life because she just loved God that much. Prot. believe none of this.
More about Mary. Both the Catholic and Orthodox revernce Mary for a variety of reason and she plays a huge role in doctrine. Both believe she remained a virgin until her death. (chrch tradition in both teach that she served in the temple from the time she was a child, her marriage to joseph was his second and was a marriage more of convinience than pasison. He was to care for her once her parents died but he was much older and had children from a previous marriage.) At any rate....protestants believe little to none of this.
praying to Mary and the rest of the saints. The EO and RC both believe in communioon of the Saints. what makes a person a saint varies. There is a very detailed process in the RC church. In the EO church not so much. Martyrdom will make you a saint in the EO church. as well as other things. Both traditions believe the souls of the departed immidiately go on to eternal life with Christ and are as real and alive as anyone on this side of the ever after. So therefor just as you would ask a friend here on earth to intercede for you you can ask a friend in heaven to intercede on your behalf. protestants generally are not ok with this.
Statues, icons and idolotry. RC uses statues. EO uses icons (very specific 2d images). These items are aids to worship. They do NOT worship the items or the people they represent. it is not idolotry in and of itself (although like all things these things can become idolotrous in the hands of some people). protestants tend to consider this idolotry. How statues and icons are used varies.
Purgatory. many catholics believe it. no EO believe it. no protestants believe it. it is not official doctrine in any church.
Sacrements. EO and RC believe the sacrements (they are different in each church although some overlap) deliver devine grace to the recipient that will help them on their journey to salvation. these are not items on a check list to get you to heaven. Protestants vary on this by tradition. Many believe things like baptism are nothing more than symbols and marriage a contract.
Sign of the cross. EO go head, heart, right shoulder, left shoulder. RC go head heart left shoulder right shoulder. protestants...very few still use the sign of the cross but Lutherans held on to it for a long time. The sing of the cross acts a simple prayer calling on the Father Son and Holy Spirit.
Salvation. Both the EO and RC believe the salvation is a process. Also at no point is there anything one can do or say that will assure their salvation. Many protestants believe that salvation is a moment in time. some say you can never lose it. some say it can be lost. Some think it is as simple as repeating the rights words and believeing God exist and that you have sinned. other think it is more complicated than that. There are probably a million different believes amoung protestants about this (which is probably what is making a simple comparrison so hard.) No body believes officially that salvation can be earned by works or sacrements.
speaking of works...The EO and RC believe that works are the manifestation of a living faith. If you ahve no works, you must not have faith and therefore should be concerned about your salvation. Many protestants believe that any works are a lack of faith. Also many believe that it doesn't matter if your faith produces works or not you are saved all the same. But the beliefs vary widely.
Christs work on the cross. Most of the Western church (protestant and RC) believes in Subsitutionary Attonement.....Christ's death on the cross is the only things that could satisfy the debt we owed God for our sin. The Eastern Church focuses more on Christs victory over satan and freeing people from the grip of hell. taking back what was his. setteling a score. I had read a really good article on this somewhere and can't find it now.
Do you have any specific doctrines or practices you have questions about?
Here is a nother chart that might be more simple.
http://christianityinview.com/comparison.html